I think the best ways to counteract this would be to do an elective at a couple of programs that you interview at and try to work directly with the program director or an influential faculty member and really wow them. At the end of the elective I would try to have a very frank discussion with them about the circumstances of your professionalism issue and how you learned from it and that you hope your performance during the elective gave them a true picture of who you are and how you would behave as a resident. I would also during this elective be as helpful, friendly and collegial as possible to the residents that you work with so that they will go to bat for you -- don't underestimate the influence residents can have on a program's match list.
Finally, do you know if any of your letter writers addessed your academic performance or professionalism issue in their letters? Sometimes, if a faculty member addresses it in a positive way and opines that they don't think this is going to present a problem for you as a resident it might help. Finally, if the Chair of your school's OB/GYN dept. or another influential faculty member really "believes in you" they might be willing to make a phone call on your behalf to help explain your situation -- but I would only use this card for the program that you really want to be at and that you think you have a good shot at.