Well, it seems to be the general consensus that the fire happened sometime inbetween 1010 and 1015, so lets operate on that theory.
To start off the proof (probably not a formal proof, but hey, you never know), we'll assume that the drawings and letters found in Lucca's house were created sometime before the fall of guardia. This paper would've had to survive first 5 years of sitting in a house (since its not framed that would imply that it was just lying around), then a fire (once again, not framed) and then another few years exposed to the elements. Paper does not hold up well under these circumstances, the heat and cold, plus other factors would completely erode the paper and most of the drawing. Thus this possibility cannot have happened short of some time lapse of some form.
If that didn't happen, perhaps the scenario went more like this: after Lucca's house was turned into an orphanage, she told the kids the story of saving the world, assuming Crono and Marle died again. Now, the line "Crono is so cool" or what-not is the tell here. You don't see kids drawing pictures of some historical figure like George Washington or Abraham Lincoln and captioning it with "Abe's so cool" or "George rocks." For the most part something like that would have to be written.
Next, lets look at a more specific possibility; ok, so this time only Crono lived, Marle is definitly dead (as she is the princess.. one would assume they would have killed her). To disprove this idea (or discourage at the very least), I invite you to picture the final scene before the fall of the castle to Poore. The poorean (sp?) army is pushing towards the castle at a rapid pace, the knights of the square table, etc. just can't hold them back any longer. It is incredibly unlikely for them to be murdering every resident on the way (only the absolute cruelest and stupidest armies did that), so the likely scenario is that, while towns are perhaps devestated, the people remain unharmed. The king orders Marle to leave the castle, contrary to some popular belief I do not believe that Marle is stupid nor a bimbo (and I don't see much evidence supporting that she is one); she leaves. This means Crono has a choice, either protect his relatively new wife and live to fight another day, or abandon her to fight a losing battle at the castle. While if it wasn't for Marle Crono would probably stay, I don't believe there is anyway he'd let her go off on her own. He leaves with her before the fall and they go into hiding.
The next key is the ghosts. Yes, they are of Crono and Marle (or so the game implies); however look at the location they're in. This is a mishmash of times and events, partially of dimensions even. I point to the "branching" theory for the structure of time in terms of parallel dimensions; that is to say that for EACH major decision with more than one outcome a branching point happens (which seems to be the way this game has treated some of the events), it is only logical to conclude that they may have died in ONE of the dimensions. One does not imply all, that would be a logical fallacy, thus there is no way you can say that the ghosts indicate anything about either Crono or Marle dying in the original dimension; the ghosts could've come from anywhere within the kalleidscope of dimensions on the same plane.
As for Lucca's letter, she is very clearly talking about them in the present tense. After all, if they're already dead then what would it matter if someone went back in time to kill them? It would've happened anyway, and as proved in the first game just because you kill something before it becomes a problem doesn't guarantee that it won't cause an even larger set of problems. You have to assume that someone with the motivation to actually do this would have the benefit in this case of hindsight. Or else why would they have any reason to actually do it?
But for arguments sake, lets pretend that the translators *didn't* care all that much about tenses or were very lose with them. Here's the problem, if that were the case then all the HUGE amount of circumstantial evidence inferred from the game's text (the parts where it doesn't give actual dates) would be completely and utterly undependable and this debate would be completely pointless. So I assume that this is not the case.
This leaves us with two possible outcomes, either a) Crono and Marle are alive, or b) Square wasn't trying all that hard to actually make the two games fit together and all this reasoning is trying to fit a round peg into a square hole.
Personally, judging from the comments made by the dev team for CC, I would suggest that it is more of a very, VERY loose sequel (also, when you result to different dimensions for a game or book you often do it because you ran out of ideas of some form or another.... but thats just my opnion (see DCs dimensions...)). However, if this is not the case, I think that its obvious they must still be alive (and they had better be.. else I'll be very, very angry with Square... how dare they kill off my two favorite characters in any video game series ever, ya... I might be a bit biased, but the logic stands on its own).
I'll admit to not being a fan of CC... personally I think it made far too little sense and didn't include the things I liked about CT (the teaming up aspects for attacks in particular), HOWEVER, as it is a sequel and the logic can prove it I believe that Crono and Marle must still be alive.
As an addition, since the dimensions all end up merging (according to the end of CC as I understand it); since they're most likely alive in the other dimension (and unless the merging of the dimensions killed EVERYONE from the other dimensions) then they would be alive in the resulting dimension anyway.
If I'm wrong on any of these, I'd love to hear your opinion on it... I think I've covered most cases except incredibly illogical time traveling just to make a specific event work like I want it... and if I were to deal with that I'd have an infinite set of possibilites (including crono going back and saving himself... I guess.. ow.. my brain hurts)