This is probably too late to implement in the plot, but an idea for a shocking occurrence just... occurred to me. It expands the "party becomes evil" gimmick but with an additional twist. Imagine this:
At some point, Magus and Glenn get warped in a strange era that looks like the Lavos's Defiled Earth from the early plot drafts. You control these two characters and must make your way fighting through all the demons, undeads, weird hostile creatures, etc.
At some point, the focus returns to the other party members, and they realize (wherever they are) something pretty disturbing: Magus and Glenn were actually sent to 1,005 A.D. and were slaughtering soldiers and villagers from Guardia! Magus and Glenn didn't know they were killing humans because they were struck with illusions and mental manipulations by the Frozen Flame, but the fact remains that they caused the Fall of Guardia! Now, the party (perhaps including the present and sane versions of Magus and Glenn) must travel to 1,005 A.D. and stop the two misled characters.
There's some additional irony as Porre tries to take advantage of the situation, yet the party essentially ally themselves with the southern nation since they have the same goals (stop Magus and Glenn). Perhaps we can mention Viper, Garai, Radius, and Zappa here, as regular Porre soldiers. The "enemy" versions of Magus and Glenn have their minds too disrupted to recognize the party and listen to them, so the party have no choice but to fight and eventually kill these past versions. However, Guardia was still mostly destroyed; they didn't manage to avoid the fall of the kingdom. Marle remains the Queen, but Guardia becomes a satellite state of Porre (to fit with its curious, apparently distinct status in CC).
Plotwise, the "enemy" characters are Magus and Glenn because they're the only ones who don't appear on the drawings in Lucca's house in CC (it would be weird to have Crono slaughter people and then a kid drawing "Crono is cool!").
Anyway, this is just a hypothetical scenario I wanted to share. I think it's definitely shocking since it takes advantage of what the player expects and twists it around into something that he probably never expected. Also, I don't know if it's really significant, but the shocking occurrences in CT and CC are not moral; they're purely plot-driven. It's also the case here (killing past Magus and Glenn doesn't affect the present versions). For moral shock, we do have the Reptite timeline story arc, in any case.
Problem is, it may be too difficult to fit this in the plot now since there isn't much empty spot to fill and since it's redundant with a few stuff (we already have two "FF warps the party around" sequences, and the Defiled Earth concept is supposed to be Crono's FF nightmare). Perhaps Glenn could have no FF nightmare and be warped to 1005 A.D. right after he tries to destroy the Mammon Machine/FF with the Masamune in the pre-nightmare Chapter. This would concretely tie the shocking occurrence with the plot and would also further explain the Masamune's corruption. This would not explain Magus's involvement though. Well, I guess Magus doesn't have to be involved and Glenn could be the unique enemy character. He'd be kinda like Dario in CC.
This being said, I'd rather keep a "coherent" storyline than try to add a very late idea at the last minute. And perhaps the "King Zeal causes the Fall" twist is more elegant, even if (or because?) it is more subtle and less slap-in-your-face. Any thoughts on what to do with this?