You took the MCAT without Organic Chemistry II? While most institutions typically state that pre-requisite classes have to be completed before matriculation, there are also reportedly some on adcoms that look at classes like Organic Chemistry as a barometer of your ability to do well in a science curriculum throughout medical school. What's your science GPA, and do you have a demonstrated track record of strong performance in science classes?
With incomplete information, I'd reason that schools would find this either not a problem or a mild, non-fatal concern that could be outweighed if you can show that you can succeed academically in medical school through your overall coursework. I've had a number of friends who have taken classes like Physics II or Biochemistry in senior year without issue.