Revisiting "Don't Ask, don't tell"

The reason given for the policy is there is no constitutional right to serve in the armed forces, and that it is necessary to exclude homosexuals because "the presence in the armed forces of persons who demonstrate a propensity or intent to engage in homosexual acts would create an unacceptable risk to the high standards of morale, good order and discipline, and unit cohesion that are the essence of military capability." And here I thought that unit cohesion was based respect and trust in the skills of the people around you.
Let us assume for the moment that homosexual sex is a sin. There is no doubt that rape is a sin, and yet "only 181 out of 2,212 subjects investigated for sexual assault in 2007, including 1,259 reports of rape, were referred to courts-martial... and in nearly half of the cases investigated, the chain of command took no action." I cannot imagine anything more harmful to the high standards of morale, good order, discipline, and unit cohesion than rape.
I think that the separation of church and state should apply to the military, and therefore they should only be allowed to exclude someone if they have committed a crime, not if they have sinned.