Keep grades consistent through the JC and the senior university later on and you should be fine. Careful with JC counselors! They often aren't familiar with the needs of premeds/transfer students. Stay on top of transfer requirements (you probably wont need the AA/AS degree to transfer.)
There aren't any disadvantage to going to a JC. PM me if you have specific questions about getting to medschool as a CC transfer student.
Most schools say they don't care if you take classes at a four-year university or a community college, but they say that with a wink and a nudge. You should really try and take most/all of your courses at a four-year university.