Someone mentioned it earlier, I think it was LnGrrrR, and he said that you need to talk to her about holding on to her past mistakes and owning up to that being YOUR mistake. I really think that's something you need to do if you haven't done so already. You royally screwed that one up. If you weren't willing to trust her after 6 years, then you should have broken up with her, no matter what she said.
You made a huge mistake by holding on to this for so long. You would have thought that since she never wants to leave your side that you could trust her again. Why do you think she never wants to leave your side? Every time she does you freak out. You hold grudges. I think you need to sit down with her and have a LONG discussion about it. Ask her for forgiveness for holding a grudge, for not really forgiving her for something that she did 6 years ago. As others have said, encourage her to do her hobby. Go out with friends, something. Encourage her to go out. Give her some cash and set up an appointment at a spa. Pamper her. Give her a full day all to herself. Don't settle for a response of, "I want to spend the time with you." Really encourage her to go out. Then, when she gets back, don't go CIA on her and ask her a billion questions of what she did, where did she go, who was she with. Just ask her if she enjoyed herself, and let her know you are glad she had a great time.
I've heard that the best thing for a relationship is to spend time AWAY from each other. It shows you and the other person how much you really mean to each other. So have her spend some time away from you. Once a week, at least. I would also add, don't push her away too much, because she might think you are trying to get rid of her. Explain to her that you want her to have a day to herself where she doesn't have to think about anything but herself.