Usually couples pay more taxes when they file separate returns, however, in your case, it may be worth it.
There are restrictions when a couple files separately, such as you can't take the earned income credit, you may have a lower Child Tax Credit, then if you filed jointly and your capital loss limit is cut in half. There are additional restrictions involving higher education expenses and adoption expenses.
Visit www.irs.gov for a complete list of restrictions and clarification of the tax code -
keyword: married filing separate