Hi,
I am currently in the process of getting my green card and immigration has requested a copy of my husband's tax return for 2011.

I entered the US on a J1 visa, not subject to FICA taxes. We got married December 30, 2011 and I was advised by a tax accountant to file my taxes as Single since I filed as a Non Resident Alien. However, my husband is about to file his taxes and he is going to put his status as "Married filing separately". Is there going to be a problem if I filed as Single and he filed as Married filing separately? Or do I need to recall my tax return submission and revise my status?

Your husband can file as married filing separately or married filing jointly.
You can file as nonresident or married filing jointly. Your U.S. Tax Return: Filing Status for Married