Well it sounds like this is your first real love and it's always hard when it falls through like that. There is also a comfortability which is why after being apart it was so easy to get back together.
The thing is she's very immature, despite her "baggage" and fear of abandonment, she's definitely not an expert in terms of dating. Are people capable of changing? Sometimes, but from the way you are making it sound she's not looking to change.
Communication is key. You have to set her down and assure her that you aren't leaving however, you don't like the way she's clingy, paranoid, demanding and controlling. If she refuses to change, then it's time to leave.
And yes it hard, and no you won't get over her by the next day, week, month, year, actually there may be a small part of you that will always care for her. But there comes a time when you have to stop fighting a losing battle. She will probably meet someone else but then again, so will you. That person may be such a 180 degree turn from the current girl you are with now that you'll wonder why she couldn't have come into your life before.
You're unhappy, and in the end it will inevitably effect your relationship. Talk to her, tell her how you're feeling, try and work things out. If things don't work out, then it's time to give up on her. It'll be hard and it will suck but you'll eventually dust yourself off and move on.