but that is the reality, 'The relationship must be subsisting at the time you apply for ILR, and you must both intend to continue live together in the future.'
but as others have said, maybe they should try relate or some other marriage guidance organisation to try and solve the problems, if not get legal advice from her local law centre or cab.
from what you posted about her father in law, maybe if she has suffered abuse or threats from her husband ??? then maybe a possible claim for domestic violence, or discretionary leave, but i doubt it ..