I don't think you can hurt your PA school chances by getting B's in an SMP.
As for your med school chances with B's at an SMP, that depends on the SMP. If you're being graded on the med school curve, B's are plenty. If you're being graded against the other SMPers, it might be okay. If there's a particular GPA above which you get an guaranteed interview at the host med school, or above which you get a solid recommendation out of the program, and you're under those GPAs, then I think it's more pointless to have done an SMP.
Take a look at Georgetown's policies, which might be the standard. They're quite open about how their students do.