Why not file MFS (or in certain cases, HoH is allowed)?  But before doing that I would ask them to check with their immigration lawyer as to whether there are advantages or disadvantages to filing jointly.  

He has minimal income, so what has she been living on?  If she files a joint return, she is taxed on her worldwide income.  That is not a concept that most countries share, so make sure she understands U.S. law.