A couple of thoughts.
1) Don't look like you're just wandering around taking classes. I don't think being a non-matriculated student is a killer, depending on your circumstances and the schools you're applying to. Be prepared to answer the question why you did it that way instead of a formal post-bacc or something else.
2) Most places cap the amount of non-degree graduate courses you can transfer into a degree program -- usually about 12 credit hours if all the coursework was done at their institution. The reason I mention this is that, if you later decide you want to roll your non-degree coursework into a graduate degree, you might not be able to bring all your credits with you.
3) My advisor recommended full-time enrollment, regardless of what I program I chose.
Really it all depends on where you're coming from (i.e., what you need to accomplish). Do you just need a refresher for the MCAT? Do you need to take the pre-reqs? Do you need to re-take the pre-reqs and enhance your GPA? Do you need to add clinical or research experience? Have you applied before and are you trying to address a specific weakness in your application?
