You could say that about a great number of characteristics that someone might be 'uncomfortable' serving beside. Why single out homosexuality?
I understand that a great proportion of potential 'military-types' are likely to exhibit this kind of 'discomfort,' so my opinion is, like yours, just flexing my own ideals without regard for reality. But those ideals pretty strongly encompass the concept that discomfort over such a thing shouldn't be patronized - particularly at such a high level of societal organization. It sets a precedent that looks silly and backwards, I think. But then, I'm a dreamer - sometimes I dream that we aren't silly and backward in this country. Then I see something like -- Tiger Woods apologizing to America for his infidelities -- then I remember where I am.