Kgee,
I had never heard of College of the Atlantic before now. I checked out their website and it looks like a very interesting college. It sounds like you are getting exposed to a very unique education (relative to almost all other colleges).
I'm glad to hear that your professor is considering offering a lab, as that would definitely be the simplest way for you to meet the pre-med requirements.
The best way to know what the medical school requirements are for every medical school is to look them up in the offical book of
Medical School Admission Requirements (MSAR). I personally used the copy that was in my college's library. Many other people prefer to have their own copy. If you are interested in only a few specific medical schools, you can check out their own websites. I just checked a few colleges and saw that now some schools are allowing you to take one semester of introductory biochemistry instead of second semester organic chemistry. A few I checked also suggest that you can ask the school to make an exception to any of the requirements, assuming you provide a valid reason why you should be allowed to vary from the typical requirement.
If I were you, and if you already know a few medical schools you'd consider, I'd try to contact the admission's office of the medical school. Give them a call and see if they would make an exception. If you do, let me know what you find out.
Your last question is an interesting one. I honestly don't recall organic chemistry being used much in medical school. Same with physics. I do think some of the basic concepts of organic chemistry were used in teaching some of the biochemistry coursework in medical school. While it often feels like much of the pre-med requirements aren't used a whole lot in medical school, I do think that most of what you learn in medical school is built upon a foundation of what is learned in those pre-med classes. In my opinion, people tend to take for granted how much of what they learned is actually used in medical school.
I wish you luck with your studies, and definitely keep us updated on what you find out and what your school does to assist pre-med students in meeting the typical requirement.