As to the question, will her income based payback plan be affected if she files MFJ; you'll have to ask the loan company.
In this forum, we have seen many cases where the loan company has forced the spouse to file MFS to keep her loan payment schedule. She'll have to decide which way is best. if you take the attitude that you eventually will have to pay the loan, delaying the inevitable doesn't seem worth giving up the benefits of filing MFJ.
