OP, not worth to cry on it.
She left, and she's gone. You have your girl friend. Doesnt matter if the other girl was just a friend or side fling, if you are serious about your girlfriend then you have to forget about this other girl. If you really love your girlfriend and planning a future with her, you should keep her happy too. Girls are possessive(very). May be your girlfriend saw her as a threat.
I have been in a similar position and I can tell you for sure that the other girl(if she is a real friend) will understand and never cross your path. If she is trash talking about your girlfriend or you behind your back, she was never a friend.
Do you want a guy to be your girl friend's best friend? You might not ask him to leave but you will always have that little fear.
Human instinct is to scare away the competition. Hence, what your girlfriend did.
Try and forget about it, there are other things in life to worry about.