I think this depends on whether or not you take any upper level science classes at a 4 year institution. If you do well in upper level sciences at a four year institution and score competitively on the MCAT, I don't think you will be at a serious disadvantage. On the other hand, if the only science classes you take are the pre-reqs and they are all at a CC, it may very well put you at a competitive disadvantage.
Although you can prove that you learned the sciences well at a CC by doing well on the MCAT, there is a perception out there (right or wrong) that it is easier to get an A at a CC (and therefore an excellent GPA at a CC will not be as highly regarded as the same GPA from a university). Almost every admissions office you call will tell you that they "prefer" to see the pre-reqs at a 4-year school.