How do you figure it hurts advancement? I don't consider vast numbers of DO students taking the licensure exam for a completely separate licensing body an advancement. Even our dean, Dr. Stowers, the most recent past-president of the AOA, said that it's really kind of silly that grades on boards are used for residency purposes. People forget these aren't placement exams - they're licensure exams.
With that said it has been, and will continue to be, my opinion that licensure exams should be pass/fail. Allowing PDs to play numbers games to knock people out just promotes laziness. I'm sorry. Judge applicants on the bigger picture. As I've said a thousand times some of the most respected, successful, and effective physicians I know are those who struggled in med school one way or another. Low board scores aren't always a product of a poor student. Real life pops up for some folks at the most inopportune times. It's a damn shame that'll be held against them for the rest of the process.
To the OP: If a program wants you they'll take you. Period. If they're not willing to take you because you didn't take the USMLE then, honestly, you probably didn't really want to go there anyway.