Need advice about work

I'm a NICU nurse at my local hospital. When I started my maternity leave I didn't qualify for FMLA since I haven't worked for the hospital for a full year yet (only a few months short). I planned on working up until the day I delivered but my body had other plans. I started my leave at 33 weeks due to sharp cervical pain and the doctor didn't want me on my feet for 12 hours at a time. Due to this, my HR department said I have to return to work after 6-8 weeks once I deliver (even though my manager said I could take 12 weeks - I guess HR has the final say). I told my doctor this and he said he will gladly write a note saying I can't return to work until after 12 weeks even though my HR department says I have to return after 8. I'm worried this will cause my HR department to fire me since I've been out for so long and I don't qualify for FMLA.