Generally this would still be better filing a joint return IF you can get an innocent spouse apportionment.
Else you are correct, it would be better to file married seperately.
You can read more about innocent spouse apportionment at: http://www.irs.gov/individuals/content/0,,id=130302,00.html
It comes to my attention that your situation would most likely more closely match injures spouse allocation. The link that I sent you to will explain the circumstances for both.
Best of luck to you.