I would actually suggest it unless you have like, uber amazing stats. MD/PhDs are incredibly competative and, although they recieve fewer applications, they accept a very small number of students every year.
Here's what I did:
I applied to about 14 MDPhDs and 12 or so MDs only. My stats suck for MDPhD but they're decent for MD (30, 3.9 gpa) so I was very selective about the MSTP programs I applied to. I only applied to ones that either required MD acceptence first or if rejected from MDPhD, I'm still in the running for MD. I've had 3 rejections from MDPhD programs so far (Duke, Cornell and Michigan) but I'm still in consideration for MD at all of them.
Don't do what I did: apply early! Especially, consider the fact that if rejected from MD/PhD, you're going to be a later applicant for MD pool. At least the schools taht rejected me did so in about 2-3 weeks so I'm slightly less screwed for MD (though I'm having my panic attack moment where I plan out what I'm going to do cause I've convinced myself I'm not going to get in anywhere).
Good luck!