Fmla now having to resign but still ill should I go back?

I started with intermittent FMLA due to figuring out what was going on with me. I then recieved a few scans of my brain and there was fluid. I had a Lumbar puncture that did not go well and i was diagnosed with a Rare Brain disorder called IIH . I returned to work for a week and i could not handle the job . I had a follow up appointment and my Physician gave me two months. I let my employer and HR department know and took them the filled out request and letter. I got an email from my supervisor that I exhausted my twelve weeks and if i did not return by a certain date i will be resigned from my position. i asked my Physician and she is not happy about that. Financially I am unable to not have a job , I have children. If i resign I will not be entitiled to unemployment. I applied for Disability but its taking a while to get that. I just dont know what to do.