Hey RX. I just realized I'm in your class, USN 2007. It's kind of funny posting on here and not knowing who you are even though I probably see you 20 times a day. I've been through this a few times in my life. Sit down and write an honest letter. Be honest, straight forward, and tell her what you told us in your post. I know how school can be stressful and sometimes you over react to the smallest things. Just ask my girlfriend, she hides the day before I take my exam. I really believe if you're honest and convey your feelings in a well written letter or card she'll understand why you did the things you did. This doesn't mean she'll forgive you and you'll get back together. But you'll get these feelings off your chest and she'll know why you acted the way you did. The rest is really up to her. Let her know how you feel and most importantly be honest.
Tell her once how you feel (hold nothing back) then let her get back to you. If the two of you can't handle the stress of school and being in a relationship together, I don't think your future with her would be too promising anyway. A long lasting relationship encounters problems and stressors significantly more than that of which you'll find in Pharm D school. Communication is everything in a relationship. Good Luck.