the bill or rights does not apply to soldiers in active duty, when on base in the barracks, and other specific situations. while in the US on leave, ROR, or whatever they are to follow the same laws and 'rules' other people do. and yes, the constitution protects their rights on civilian matters.
the military has a seperate system to deal with special cases where there might be treason, threats to national security and stuff. your assertion that soldiers follow different rules is wrong. they only follow different rules while on active duty.
and shame on you for implying that it is the military's duty to foster homophobia by segregating openly gay service men/women.