Matthew, the answer is yes. As a former commander, I can tell you that the military has plenty of tools to police behavior, whether by heterosexuals or homosexuals, that might harm a unit or other service members. These include rules against fraternization, abuse of authority, etc. People who take the same oath, perform the same duties and incur the same risks in service to our nation should be treated the same. Civil servants are not required to share showers and hot bunk with one another.
Civil servants can quit their jobs and go home at night.
Soldiers are bound by military law to do what they are told. They can't choose roommates or shower mates. The military is not a job but a way of life. It is marked by a general lack of privacy, little individuality, and self sacrifice. Soldiers are expected to adhere to unforgiving organizational values and behaviors.