Are you currently in the first year or two of your PhD? I think that switching to a MD/MS could put your program funding in jeopardy. Also, your research mentor is going to be writing you letters for residency programs (along with other people who would know about you switching from MD/PhD to MD/MS). I'm curious why you want to switch though. Sure, the PhD is a long deal, but most people drop it altogether, not get an MS instead. Is it because you could get an MS now and get out? OR do you just not want to spend as much time doing research?
Personally, I'd stick it out and get the PhD. But, not knowing your current situation, how much research you've done so far, and whether your PI is awesome / sucks, I couldn't say for sure what I'd do in your situation. Are you having second thoughts about a research-based career and wanting to just do residency and clinical?