She was on a J1 till 8/2010 then we married. She filed her 1040NR in 1/2011 and it was already accepted. Now I wanted to file jointly but she SSN shows that she already filed. What else can we do to file or amend jointly?

Your wife will need to amend her return and change to married filing jointly.
Since she was a non-resident alien in 2010 you can only file jointly if you yourself are a US citizen/permanent resident/resident alien and you attach a statement to your return making the choice to treat your wife as a resident alien for 2010.
http://www.irs.gov/businesses/small/international/article/0, id=96734,00.html