What happens to Magus, then? Do we automatically fight him at North Cape, or do we skip the encounter entirely and after the Blackbird is destroyed the Black Omen rises after the Dalton battle?
As for the option to save either Crono or Schala, I would vote against that. I foresee too many complaints from people who like both Crono and Schala.
And, for the record, we need to get the 8th PC up and running so that we can have Magus back. It's just not CT without Magus in the party.
EDIT: I just remembered that the choice reminds me of a part in Mass Effect where you have to choose between two crew members, one is saved, the other dies. IMO, that will be my reasoning behind my opposition. If anything, have her survive the incident somehow and turn up after the Black Omen rises.
My idea:
After the Blackbird goes down, go to North Cape to meet Magus. You can either kill him or recruit him. Go to the Epoch and watch the Black Omen rise. Then go to the commons and find Schala. You can either recruit her now, or have her stay behind and oversee the construction of the new world. If you recruit her, Magus will remain behind. You should be allowed to switch between the two, but never have both at once.
Like it?