It's like that in quite a few schools, particularly in CA. Just contact the med schools that you're interested in applying to. They are used to the question, know the situation, and yeah, it does wind up being okay and meeting the requirements.
My school is that way. We have two quarters of lecture with lab required with it, then the third quarter lecture and lab are separate. All the bio majors that are premed didn't take the third quarter lab so I'm pretty sure you'll be fine (I was biochem so I was required to take it).
OK, twist on this question:
I may retake organic for 1) a better grade and 2) a refresher so I can improve my MCAT score. I took it in 96-7 and got straight Cs with lab. SO if I do a repeat organic class (or 2) WITHOUT lab would schools consider it?
I always did great in lab (it was fun, like cooking) and quite frankly my lab grade buoyed up my awful test scores.