In order to give the borrower the benefit of not having to re-apply, decision your loan with the condition that it cannot close until you have a paystub confirming her back to work. However, that is only if she does not qualify at the current income being received.
I concur that if the borrower IS receiving any income from that employer, full to whatever percentage, and they qualify, then you make the loan with a letter from the employer that she will be returning at at least the level of income or greater and on what date, coupled with a signed intention letter from the borrower.
You are NOT bound by FNMA or FHLMC rules, meaning you can be overly cautious. They issue guidance on what they will accept. They do not legislate that you follow the rules, without overlays. The issue lies if you become disparate in your underwriting and lending or you go against your companies written policies.