As the wife of a retired Navy man, I have been through something akin to what you're experiencing. My husband was gone for usually about seven months, then back home for about a year at a time. During the year at home he often had those little two week trips "out of town" (actually out on the Pacific Ocean on a ship). Those short trips were by far the hardest on us.
All I can tell you is that constant 'preparation' is the way I dealt with it. We talked all the time about what daddy did and what was coming up next. It wasn't like being morbid about the fact that he'd be gone, just upfront and practical about what was going to happen and how we'd deal with it. About a week before he was due to leave, I'd have a sit down talk with the kids and say something like "next Tuesday Daddy will be going out to sea for two weeks. We need to have as much fun with him now as we can and be ready to take over doing his part at the house while he's gone." It was never easy, but by including them that way, I think it made the transitions smoother. My experience was that it was harder when he was coming home, because we had developed our own little routines while he was gone and had to remember to really include him in family life while he was home. So I tried to put the emphasis more on what we could do for him and what he had missed by being gone, than on what we missed by him being gone. I realize that you have to get this down to the level of a two year old, but maybe if you can get those older boys in on it with you and talk to them in her presence, she might pick up on it better than if you try to directly deal with her.
What the other person said about your husband getting a different job sure may sound tempting, but that isn't always a viable option. Kids do survive these situations and the best thing is to make the best of it yourself and help her through it. I also found that my own reaction to my husband's leaving was a key to how my kids responded. I let them know it devastated me to have him gone, but that we'd get through it together. And I always let them know that it wasn't any easier on him than it was on us... in fact maybe worse.
Just remember, you're not alone. Think of all the military wives and families with their guys (or gals) in Iraq or other parts of the world right now, and know that just as they are surviving, you and your kids will too.