Don't really see what the problem is here to be honest. He thinks it's immoral, that's his right. In a country as religious and dare I say fundamentalist(in parts) as the US, don't ask don't tell probably works pretty well for the armed forces.
His beliefs, he can believe whatever he wants, be it a diety or some messed up view on someone elses sexual preference.
He's entitled to his beliefs, but the problem is that his and other's beliefs are being implemented as discriminatory policies. "The newspaper said Pace did not address concerns raised by a 2005 government audit that showed some 10,000 troops, including more than 50 specialists in Arabic, have been discharged because of the policy."
What people do in the bed room and the way they live their lives are up to the person it involves and as long as they are not harming anyone or taking advantage of an underage person then i dont see who he is to judge on morals.
How about killing people, then? Perhaps General Pace would have a bit more credibility if he condemned the torture of "terrorist suspects", for instance. But we all know that morals and souls fly out the window when paranoia, expediency and financial profit sashay through the door. Anybody home? Ain't nobody here but us sociopaths.