road--
obviously she misses you, and wants to spend time with you. however, letting her know that you care about her, and appreciate her, even through the smallest things, shouldn't be construed as a 'time-sapping event.' and maybe you just wrote that because in that moment, you were fed up. if not, then your best option would really be to re-evaluate the relationship as it relates to your career. on the flip side, does she really understand what is involved in flight school? does she know your hours, the pressure, the competition-- the fact that this is your life, and this is your shot to either make it or break it?
just because she's crying in bed doesn't mean that the clingy, needy impression we've gotten is how she is 100% of the time, but if she's like that more often than not, being a navy girlfriend probably isn't something that she's cut out for.
if she really has no clue about this, as you say, then you're both to blame-- her for not finding out on her own, and you for not telling her. you may be 'committed enough' to live together for a summer, but if you're not communicating, then there's no way this will last. if you do part ways, it will probably be best for both of you in the end.
has she run through the NATOPS with you? would she understand what she's reading? does she know much about EP's, FAM's, maneuvers, etc? have you taken her to an airshow? does she get it?
if you don't have the time to give her, and in four days can't either find the time to make, or to have conversation about the strenuous demands already placed on you, and that your time is at a premium, AND if she either doesn't understand that, or isn't willing to work with you, then yes, you have some serious thinking, and talking to do.