if you are not getting your medical school (do or otherwise) fully paid for AND you really want to do research... my suggestion would be to do your PhD at the best place that you can get into.
Most DO schools provide a fine medical education; however, they typically lack big research reps and thus big research names. Example: PCOM has a DO/PhD program. In 2005 they had 4 NIH grants. North TX had a decent #, but not anywhere near your typical big research U.
If you are footing the bill for medical school, there is little/no advantage for staying at your school for the PhD. I know of several MD schools that will let you take time off after ms2 to get a phd. If you can get into a DO school, do well in year one, and have a bit of research background, you can probably get into a university that has more funding (thus opportunities) for your PhD.