Daniel, you've made some very good points, which I agree with for the most part.
The other thing, I suppose is, that it's true that Lavos has planet destroying power... but at a far distance. For example, the US may have a surfeit of nuclear weapons, but wouldn't dream (except for maybe the gravest of counsels of despair) to launch them if their own soil were under attack - it would injure them too greatly. Likewise, considering how near they stand to Lavos, it may just be he cannot use his most powerful spells and sorcery on them due to their proximity. As such, Crono would not have to withstand such high forces as might otherwise be attested to him. Taking it down to plot, it may just be a case of David and Goliath, rather than, well, Goliath against Goliath. Crono didn't win because of superior might, but by using tactics that Lavos could not counter well. Okay, David and Goliath wasn't meant to be about that, bad example. Say, rather, the second Death Star from Star Wars. It had the power to destroy planets. Yet Wedge and Lando, flying an X-wing and a heavily modified correllian transport, destroyed it - a station 120 km across. Look at Crono and Lavos the same way. Taken at sheer power, Lavos is a hundred times their greater. But what Crono did was engage him at point blank range - still a peril (for which he needed his great power that he gained through the journey), but annulled the greatest portion of Lavos' strength. Then, having blasted a hole into it, proceeds to combat its more vulnerable self under its mighty battle-armour. Just like the Death Star, which stood immortal and unstoppable for a time, but once breached was destroyed by a proton torpedo and a concussion missile. 120km of space station destroyed, because it was in-apt to combat the tactics it was presented with. The same is true for Lavos. Crono's victory wasn't all might - it was cunning, and knowing how to fight. (Now, Crono, I'd figure, is probably equal to or greater than the true Lavos inside... but from the way I figured through this, is no match to the planet destroying bio-armour he is encased in.)
I think it is a reasonable assumption that Lavos was unable to apply the entirety of its planet destroying energy onto a nearby target, not necessarily because Lavos would damage itself, but because it could not focus it's attacks.
It was stated that the Core contained the majority of Lavos's vitality, but that doesn't mean it has greater destructive potential. Lavos is a single organism. The shell might be specialized in widespread destruction and durability, while the Core is the source of power and intelligence.
Consider this: Lavos is essentially unrivalled in power. The Entity, for all of its ability to manipulate time and space, was helpless to combat Lavos directly. If Lavos were to meet it's equal, such a confrontation would probably destroy the earth (for example, if the Death Star appeared in orbit.) Rather, the time travellers were able to bypass Lavos defences and invade its body, not unlike a microorganism, and combat the Core.
I think that beyond a certain level these sorts of epic battles hinge on the ability to manipulate elemental forces with finesse rather than brute force. For example, Crono's Luminaire may actually be consist of a highly focused release of magical energy, while the "lightshow" is simply a side effect. The striking edge of Crono's sword might exceed pressures found within the sun, but the blow doesn't have to carry so much force with it.
Now, as such, it means that Crono isn't all THAT powerful. There is no neccessity saying he can't be killed. Yes, he may be a great hero, but he is still human. Grey, you brought up the example of Beowulf. Yes, he was very strong, and killed Grendel and his mother with his bare hands... but still he perished to the dragon! And Sigurd, the bane of the dragon Fafnir, who became nearly invincible by bathing in the dragon-blood, was killed by treachery. Tolkien's Turin, a mirror for Sigurd, who performed similar feats in the killing of a great dragon, and was amongst the best of mortal warriors (and, indeed, was fated to kill the Dark Lord Melkor, Sauron's old master, at the Last Battle), died - in grief and horror, casting himself upon his own sword. Herakles, mightiest of the Greek heroes, did not meet any natural or peaceful end. The hero that defeated the great hydra, who went to the ends of the earth to fetch the apples of the Hysperides, and for a time bore the weight of the world in place of Atlas, and later took Kerberos from Hades itself, was killed - by a dead foe, no less. The Centaur Nessus, in lies to Herakles' wife, convinced her that his blood was a love charm - but when she attempted to use it, sending her beloved husband a cloak dipped in it, the hydra venom that had been upon the arrow when Herakles killed Nessus, burned into the hero's skin, and painfully killed him. Subterfuge, again, is the bane of a hero no one - not the giants themselves - could stand against. Great Aias, second only to Akhilleus at Troy, who was like a wall in the defence of his fellows, died by his own hand in remorse. There are manifold heroes that can be mentioned, many having superhuman qualities, who nonetheless succumed to death (though apotheosis on occassion follows that.) I do not see how Crono need be any different. Indeed, like Herakles, it could even have been a minor foe, one he could easily kill, that was his downfall. No great earth-giant, no boar or bull - a ferryman centaur.
I really like those mythological examples, by the way.
Of course, the time travellers are mortal. Crono demonstrated that fact already, although history could be changed in that instance.
Crono definitely did not have planet destroying power, however he also definitely has abilities which exceed those of ordinary people. Although the time travellers may not have had to face the full extent of Lavos's power, it was still a formidable foe. If, to pull a number out of my hat, Lavos's full power was 10^14, where the time travellers would go on that scale is up to interpretation.
I think that the time travellers are around the city destroying level. Going all out, they could probably flatten, say, Truce. One of Lavos's full power "Destruction Rains from the Heavens" lasers would probably do them in and something like Lavos's impact in 65 million BC would definitely kill them.
It's just... trying to imagine him taking on an army like that just looks rather silly to me. If he could fight them all by virtue of his sword-skill, like the way they show the assault on the royal palace in Hero, that could be... but otherwise... I don't know. It would just look too cheesy. I'm willing to chalk up all that power to simple game mechanics. Imagine it... actually imagine how that would look. There's a not so fine line between heroic and overkill. To give Crono the ability to destroy an army is almost certainly overkill.
More importantly, it is damaging to the story. What it does is take away his vulnerability, and thus his humanity, minimizing the impact of his character. A hero's relationship with death is probably his most important. In most myths and legends, it is a continual struggle between the two, with the hero victoring for a long time. Herakles wrestles and overcomes Thanatos, for example. And for the Greek hero, the highest point of achievement is a Katabasis, a descent and return from the underworld, a sort of victory over death. Herakles does this, as does Theseus, Orpheus, and Odysseus. Later, Aeneias does as well. The point is, to remove his vulnerability is to remove a very important - almost marking feature - of a hero. In the end, the hero always falls prey to death - and, in some cases such as Herakles or Oedipus, has the final laugh with his apotheosis. To make a hero too powerful is to remove his humanity, remove this examination, and thus remove his relevance. After all, Akhilleus isn't immortal - that was some later rendition. Any arrow, any sword, anywhere, could have killed him. His examination on courage and the chance of death is perhaps the highlight of the Iliad - to have made him fearless and unstoppable would have removed a crucial element. So it is far more interesting to say 'what kind of ill-fortune could have killed so mighty a hero as Crono', and consider it in wonder, than to say 'he's nearly immortal so it couldn't have been the army.'
The thing is, the comparison with the Death Star isn't in-apt. Yes, it appears to get stronger... but it doesn't. The outside has a hundred times the power of the interior, it's just all meant to be used at long range. Close range, it appears weaker, thus the appearance of strengthening as it gets inside.
The extent of the time travellers abilities are difficult to judge, because the only source of information is the happenings in the battle system, which is problematic. Consider some of Crono's feats: he was withstood bullets, missiles, lasers, etc. Although we can't quantify it, he's pretty tough. Robo and Ayla can toss dinosaurs into the air like beach balls. Of course, Crono is vulnerable to attacks, but mostly from powerful foes such as the monsters in the Black Omen. In full battle dress, with all their weapons and equipment, the time travellers are probably a match for any of Porre's forces which we have seen. Of course, the time travellers always have a change of dying. I'll just say that Crono and the others are
less likely to have fallen in battle.
Against an attacking army, Crono could use his magic to decimate the enemy lines and turn the tides of battle. (You need troops to hold territory and Crono can't be everywhere at once.) Fantasy literature is filled with examples of magic users completely destroying entire armies, so I don't find this
too outlandish. However, as Sentenal stated, wholesale slaughter isn't Crono's style. If the time travellers were involved an a direct conflict, they would sneak into enemy territory, disrupt supply lines, and infiltrate the enemy's stronghold. Of course, with the possible involvement of forces outside the normal flow of time, there is the potential for bigger nasties which would give the time travellers some real trouble.
Assassination or abduction are more likely methods the time travellers could have been dealt with. The use of poison or other subterfuge would be able to bypass the their defences. Lynx and Harle attacked Lucca when she was the most vulnerable and succeeded in abducting her. Therefore, the time travellers are not invincible.
Throughout Crono's adventures, he was always been in danger of dying. (Although we can simply reload a saved game.) However, to all appearances, Porre's soldiers and weapons are greatly inferior to any of Crono's prior opponents. I think that for Crono to be slain by a common soldier would be an unfitting end. It would be like if Odysseus was run over by a horse cart.