I've only been married a bit over one year, but am now 32 and during my time in the military I went through a ton of girlfriends because I'd be home for 3 months and gone for 2 with a few days warning sometimes. Not too many girls liked me disappearing before birthdays and getting a telephone call from Nigeria a couple weeks later. I learned a lot from this however.
You're right to say you can't keep her from going and I understand you don't want to prevent her from doing this. She has to recognize that you're better together than apart and that she loves her life with you. I had some problems when I first got married because I had a lot of independent/adventure times in the military and didn't realize that I loved being with my wife more than I enjoyed going to Honduras with my crew. Your girlfriend might be having the same issues. It took another long trip without her to realize that I was not the same anymore. Don't prepare for a breakup because that's going to set your heart against her and a breakup will happen. Love her and continue your relationship as close as possible to what it was before she moved. Also, don't ever remind her of this in the future because it's not that you were right and she wrong, but she needed to appreciate what she has with you. Sorry for the ramble but it's not a simple subject.