I can relate to this on so many ways. First, the "if only we weren't thousands of miles apart" part... and then the whole difficulty with communicating the whole unvarnished truth part.
I've had to tell myself, this is the way it is for now, so I need to find a way to get okay with it. This doesn't mean pretending not to be in pain sometimes. After all... thousands of miles away, you miss each other, you don't get that physical connection... it's hard enough without adding other stuff into the mix. I'm finding that sometimes I just need to feel the pain. This doesn't mean vomit it all over my hubs, but trying to hide my feelings from him doesn't work either. It's similar to her not wanting to tell you things because she feels you'd be hurt.. .but by keeping them from you she isn't giving you the chance to deal with the issues and learn what you need to learn and grow how you need to grow. Growth and change is not easy, and you can't sugarcoat it. Also, by not telling you what's going on, until sometimes later, she's creating a situation where you don't fully trust in what she's telling you. THAT you most definitely need to express to her, because that kind of second-guessing the other person is never a good addition to the relationship. Yes, by telling you she might have to deal with you being in pain about it. She needs to understand that she can't avoid your pain, and you can't grow through and maybe out of your pain without these steps.
I think sometimes my hubs wished it would just be "easy peasy", and he could do what he wanted and I'd dance around merrily, singing a happy tune. (Sorry, a little too much Disney this weekend!). Point being, you have to go through the process-- and so does she. By being forthright with you, and letting you feel your feelings, you both will eventually grow enough so that you know that sometimes it will hurt but you will get through it and she loves you. And she will get to the point where she knows sometimes things she does will cause you some emotional moments but that you will get through them, and process it and come out better on the other side.
I think sometimes we get caught up in the details. He/She did x with the other person Y times and in Z positions. It's easy to let yourself get caught up in that and work yourself up. I'm finding that it's the big picture sometimes... he/she loves me. We are together. By her doing (whatever) with someone isn't going to change that. And that is what you two are building... the knowledge that someone else in your life won't negate your love. In fact, sometimes it will build it up further.