It is very possible that MFS is the best outcome for them and it sounds like you've run all the numbers.  Here are my only concerns:

1. Are you in a community property state?  If so, they have to claim the income under community property rules.  Otherwise, you are fine.

2.  If an original return was filed as MFJ, then you need to get the superseding returns done and filed before 4/18 or they won't be able to file MFS.

Good luck!