It's good to see another gator here. There are a lot of us using SDN.
One-semester organic WILL NOT put you at a disadvantage when taking the MCAT. I enrolled in that course and scored a 10 on the bio section both times I took the exam. Dr. Deyrup is a great guy. Unlike most organic classes, you won't have to memorize a single mechanism!!! You will learn fundamentals that will help you approach any reaction appropriately.
If you take this class, however, you WILL have to take the bioorganic chemistry class that follows. This course is BRUTAL!!! There are a few instructors for it, unlike the one-semester organic class. I had Dr. Richards. Some people like the guy, but I didn't care too much for him. He hates pre-med students, berates people (he called a guy dog-face in my class) and makes people cry. During my final, at least three girls were crying. The class average at the end of the semester was a 44%! I know this because I was only slightly above it. If you choose to take the class with him as your instructor, prepare to work like you have never worked before. Chemistry is my major. I'd like to think that I am not stupid, and after reading each chapter three times I earned my only C.
Ok, enough with the bad memories. You'll have to take both classes before applying to med school. You should take both before taking the MCAT, though I think you might be able to do well without the bioorganic chem class. Good Luck!