That's where I believe the whole school of thought goes awry. It is automatically assumed that the problem is going to be with straight male soldiers in close proximity with gay male soldiers. What's going to happen when a gay soldier wants seclusion from his/her straight comrades? Or, when straight females refuse to share billets and latrines with gay female soldiers? Don't say it can't happen, because it's far from a impossibility.
You end up with the same issues that exist with providing privacy for all soldiers. You don't have to be gay or homophobic to desire privacy. When it is possible, the military does its best to provide this. When it is not, this goes in the suck it up category. Sometimes, you are asked to go without sleep for days at a time, wear dirty clothes, kill people, and watch your friends die. If this "suck it up" concept is confusing to you, there is a VFW chapter near you and I am sure they will be happy to help.
When shower facilities are limited, accommodating female and male soldiers cause issues. Sometimes this is dealt with with shower schedules. Some small outposts do not have adequate facilities and female soldiers are just not posted there. These are practical solutions to practical problems.
I think you miss the point of inclusion in the military;
Rome did not offer slaves a route to citizenship through military service because they respected their rights - they needed the bodies. The racist old boys club of the American military caste did not include black soldiers because they liked them - they did this because they needed the bodies. Israel does not have women serve in combat roles because they want to see their daughters killed - they do this because they need the bodies.
Last I checked, homosexuals made up somewhere between 10% and 30% of the population, depending on who you listen to. From my own experience, I would say they make up a much larger portion of the females in the military then either of those numbers.
I also think you miss the point of regulatory inclusion;
No law nor amount of homophobia has ever kept gays out of the military. Given that this is a fact, policy must be set based on creating the most functional military we can have. This is no different then any other form of prejudice - ethnic, racial, religious, etc...
Serving your country is not something where you get to pick teams. Prejudice and tension will always exist in any military called from a diverse nation. It is one of the few times in your life that you be will asked to set aside your differences and serve the common good. Doing this is part of what it takes to be a solider.
Personally, I would be offended if being gay was a reason to avoid military service - if you expect to be reap the rewards of living in this country, I expect you to pay the same price for that privilege.
That anyone, be they gay or straight or purple or made of jello or whatever, would choose to serve deserves respect. If you have not made the same sacrifice, your ground to judge is shaky.