You don't have to be angry and treat her with vengence or rage. Telling her that you would prefer it if she left you alone is not mean spirited at all. There isn't any more you and her, it's just you now and you need to look after your best interests. If her still being in your life is messing you up, you have to let her know that you need space. Which may be confusing now after being accepting of her behavior, but it's just being honest. I can't help but feels like she knows she has you and if things don't ever work out, she think she can play upon your feelings and you will be there for her. It won't get you anywhere that you want unfortunately in terms of getting back together though.
Like they said, more power to you for handling this with a cool demeanor. I can't help but wonder if it's really tearing you up on the inside. A couple months in a locked room can be pretty depressing, and I know it feels great to talk to her, but friends? With her ex when she's still dating a new guy? Doesn't add up.
Waking up next to a beautiful girl,
Step outside and say hello to my beautiful world.