I would call back and check on this. I'm on IBR, and my husband and I file together, and that hasn't been a problem. Now, I'm the primary income earner and the one with the largest student loans, and that seems to factor into their recalculation each year of what I'll be paying in the upcoming year for loans. My guess is that you might only have to file separately if you are separating some of the calculations for income, but I'd definitely check further.
http://www.ibrinfo.org/faq.vp.html#_The_calculator_indicateshttp://www.ibrinfo.org/update_marriedborrowers.vp.html