I'm a big believer in school being what you make of it. If you get good grades at HES, I don't honestly think that med schools will look down on the fact that it is the "Extension" school. From what I've heard from a friend in the program, the course rigor and expectations far exceed that of any regular four-year colleges that I'm familiar with anyhow.
As far as your particular situation goes, you have to be realistic and know that your GPA (both cumulative and more strikingly, your BCPM) are far below average for most U.S. allopathic medical schools. Even if you were to retake all of your pre-req classes and throw in a couple of upper-level sciences, and get "A's" in all, your GPA will still most likely be below average. That is not to say that all is lost. Many an applicant has been able to overcome a sub-par undergraduate GPA by showing an upward trend in current coursework, and more importantly, by rocking out on the MCAT. Realize that the MCAT is testing your Gen Bio, Gen Chem, Orgo, and Physics knowledge, so if you aren't quite up to snuff in those areas (as evidenced by your course grades), you really want to work on those areas before you even attempt it.
Other options you may want to consider are U.S. osteopathic schools and Carribean med schools, which look for different qualities/stats in their applicants.