There's a number of options for doing research while in medical school. You're correct that most students only do clinical research in medical school, but the amount and quality of clinical research is often reflected in the amount of NIH money received. It tends to be that schools strong in basic science research are also strong in clinical research, and as a result "research oriented" typically means either. Many students take a summer to do research, and typically this is clinical research as doing basic science in a summer tends not to yield much results. However, some students will also do a year out to do basic science research, and this looks very good on a residency application. This means that you do not have to get a PhD to do meaningful basic science research. Options for either summers or years of research will depend on the amount of research going on at that school and the amount of money available for medical students to persue that research. Some primary care oriented schools may not have as many options or as much funding for their medical students to persue these things.
Just as an aside, the most competitive residency programs are very research oriented and tend to pick students who have done research. Besides that, it's no mistake that the schools who bear the most weight (whatever weight that is is arguable) when it comes time to apply are the schools that have the most research going on. One could argue that academically based programs will breed academically based physcians. It's an even stronger argument that primary care oriented schools are trying to produce primary care physcians, and therefore training to become researchers or academic physicians may be lacking.
None of these opinions are set in stone and they're all generalizations that won't apply in every case. Still, I think it reflects why one might choose a medical school strong in research.
Good luck!
PS: mmz6 is right. I never did mention MD/PhD, but all the top research schools have MD/PhD programs. Also, there are a few students who start or continue to do research (clinical or basic science) during medical school classes. I think they're insane, but it is possible.
