Neil,
If I were you I'd bite the bullet and seek out the advice of an eldercare attorney. I know y'all aren't elderly, but the same rules apply. You are looking to save your assets. Call your ALS Clinic and ask the social worker if they have a pro bono lawyer they can recommend, you never know. Also, in our state we have attorneys that will handle issues for the disabled either free or at a lower rate. But, you really need the advice of someone familiar with laws concerning the elderly and keeping what you've got.
You don't want to go thru the hassle of getting a divorce to find that it doesn't really matter one way or another to the state of federal government. Laws vary from state to state.
As far as SSI, just living with someone that has income can reduce the amount of SSI she would get.
http://www.ssa.gov/ssi/text-eligibility-ussi.htm
I'm very sorry y'all are having to even think of such issues. It is really hard to hear about PALS that are young with young children. My husband is 49 and our son is soon to be 8.
Good luck and I hope you will keep us posted on how you handle this, as I'm sure there are others going thru the same things and could use your help.