I wouldn't go as far as to say, "It is common fact that med schools look down on pre-reqs taken at a cc." What is common fact is the second part of your statement; it looks real weird if one is already at a four year. There are plenty of people on here that started off at a cc and took some of their pre-reqs there and came out just fine, often times without mention of it in interviews. Now, if you are intending to go to Harvard, then yea, it will hurt.
Anyways OP, orgo at cc's is usually class and lab together or nothing. You usually can't take labs independently. Further, IMO, it is never a good idea to take split sequences. If you start a sequence in orgo at one place, it is a good idea to finish it there. 
Bottom line; if you want to take calc, English, psyc 101, etc. at a cc over the summer then that probably won't hurt. But avoid the pre-reqs.