It is possible that people that are in relationships that are based on solid principles can have members of the opposite sex as friends. It is just a trust issue that many people never come to terms with that make the majority of people be wary of their significant other having friends of the opposite sex. I think you should ask why is she trying to reconnect with you after a hectic time in her life? It may be uncomfortable but you could sit down and ask her why she suddenly is interested. I don't think people feel guilt for nothing so you should ask yourself what in your past may be causing this sort of response now.
Now as for your second question, I've been contemplating this question to. I've decided the route in life to go is the medical one. I will be going back to college for the time being so will not see the inside of medical offices or hospitals for atleast another year, as I'm going into the nursing field which fast tracks you into offices and hospitals. I wouldn't say you were being irrational by protecting yourself against the other med students because there are a lot of hidden emotional minefields out there but I would atleast try to see who within your class peers you could share tid bits of information with who respond in a positive way. There are a lot of "deeper" people in the world, someone just has to show them the ability and oppurtunity to express their "deeper" self.