I think that you will never feel better about this until you say something to her and get it out in the open.
You can't have a lasting relationship, if you aren't willing to communicate.
You may hear something good, you may hear something bad, but isn't either choice better than sitting there holding it all inside of yourself?
Don't mention looking in the diary as it will lead to her feeling violated. It is something that happened awhile ago and it dealt with her feelings rather than her taking any action so don't try and create a problem where one doesn't exist. Yes your feelings are hurt but she is with you and has been with you all along...that is what really matters. Get over your hurt feelings and strive to be the best boyfriend she could ever have...