I can't address the whole long story.
However, there was no reason to file separately when he was disabled. SSI (supplemental security income) is needs-based and having a spouse income might affect eligibility, but SSDI (social security disability insurance) is earned by working and can't be taken away even if you are married and your spouse is a millionaire.
If he never filed tax returns when you were single, that is problem that could result in an audit at any time. But the fact that he might have tax problems from before the marriage is not an issue if you file correct joint returns during the marriage.
I suggest you speak to a different tax professional who can review the entire situation.
Filing MFJ for all the years after you married, including amending all your prior returns, is probably the way to go. But you may not need to go back farther than 3 years.
