This is an immigration question and not really a benefits question. You seem to know you are entitled to those benefits -- you are just worried that taking them will cause problems.
If you have used your EAD (employment authorizaiton document), you have "bet the farm" on your I-485 being approved. Using your EAD voids any other status which may allow you to stay in the country legally, such as student (F-1) or various employment based visas (e.g. H-1B). Your only hope to stay in the country after using the EAD, is that your I-485 is approved and you get to be a citizen. If turned down, you must leave immediately. (This is why it is critical for work visa holders to emphasize they are using their work visa and not EAD to obtain employment while an i-485 is pending.)
I do not see how collecting benefits can affect your I-485 (you are still considered an employee of the company while on disability and leave) -- but you really must consult an immigration lawyer about this. I would also recommend ammending your I-485 to add the reason that you are the mother of a US Citizen (your child). This ammendment is not an 100% sure thing to get to be a citizen but, in your case, where you are gainfully employed and the mother of a US Citizen, I do not see why INS would turn you down.
Good luck with your situation. I want to emphasize that this is not legal advice. It is just a general comment on an interesting senario. You must really see an immigation lawyer and give that person the full details of your situation.
