Personally (I may be a bit biased though
), I think it's an asset to have an MBA when you are applying for residency. But I'm not the only one. I've talked to numerous deans that think it truly elevates your application-and these people don't like med students to take time off to get an MBA (go figure!). The key is how you present it. Have you been able to demonstrate an application of your MBA to medicine or did you concentrate your time on I-banking? If you have no healthcare applications of your MBA, I think you minimize this during your interview. But if you did something like start a clinic or figure out a way for more uninsured to get insurance etc. then I you highlight highlight highlight.
Regardless, they will ask you and you have to have an explanation, so prepare for it. Practice it and communicate with your deans about what to say. Chances are that you've already explained this numerous times so just refine your shpiel.
In terms of being a "flight risk" I think the easiest thing for an MD/MBA to do is to leave right after med school. If you state that you are committed to being a clinican and have good reasons why you want to become (in your case) an orthopod, then not only will they
NOT see you as a flight risk, but they will see you as an asset. Keep in mind that many residency programs now offer fellowships in administration. Additionally, if you can't keep your doors open, you can't see patients. How do you keep your doors open...you have to know how to handle the $$$.