OP, I will share with you my experiences as I went from HS to a CC, then to my state university along the way to med school acceptance.
Before the long-winded story, I'll give you my advice. Call a few schools that you think you might apply to (not just Harvard, Hopkins, and Penn), I'm talking about some of the public CA schools and ASK THEM if CC credits in the premed prereqs are OK with them. Now a little background.
Out of HS, I lived at home and attended a CC. I transferred from there to a state school (guess which one) and finished a BS (in math). I then went to work for the USAF for 5 years. During this time, I completed at PhD (also in math) from the same state school. After this, I went to the Bryn Mawr postbac premed program and took the basic sciences. Before I got there, I went back and forth about re-taking physics since I had taken it at the CC 8 years earlier. I didn't think it was necessary due to my graduate work, but my adviser at Bryn Mawr advised me to do what I described above. I did and was surprised at the results. My alma mater even told me that they would NOT CONSIDER MY APPLICATION IF ANY OF THE PREREQS WERE FROM A CC!!! This sealed the deal for me, and I ended up retaking physics. It was kinda silly, but I took the easy A and tutored a lot of my classmates along the way. 🙂
In my opinion, I think the CC thing (which has been debated a lot on SDN) really matters more to public med schools than private ones. Public school have to justify to the taxpayers and the legislature who they accept, while private schools can do whatever they want. This cycle, I was invited to interviewed at 12 out of 14 schools that I applied to (2 public, 9 private). One public school asked about my attending a CC. Nobody else asked a thing about it. If anything I was complemented for being a 1st gen college student and going from a CC to grad school, yada, yada, yada.
The most important thing is to make good grades, be a good person, and be maximally informed (not just from SDN, but from the horse's mouth too. Call some schools!). Keep in mind that what worked for me, might not be what works for you. I had a very non-traditional path to med school. Either way, I hope this is helpful. Write if you have questions.
Have fun and good luck,
Gator
p.s. I ended up getting accepted at my alma mater and a few others places (including Harvard). Just getting to interview there was a life-changer for me. It confirmed that you really can start out at a little community college in some nowhere town and by working your tail off and being polite, achieve anything you want.