Nerd, the problem was already there. Before "don't ask, don't tell" Gays had to be secretive because they were subject to immediate dismissal if it were discovered and there was an active effort made to ferret out homosexuals in the armed forces.
They were considered to be more suceptible to blackmail because if they were "outed" they were ruined. No one would knowingly hire a homosexual and some were even shunned by their own families.
I realize that this is normally NOT the case today in most cases but when you are dealing with intelligence and national security you do not take chances.
If it is of any consolation to you, Gays are not the only ones who are targeted. Drunks, compulsive gamblers, adulters, in short anyone who does things that would either compromise their effectivness or might give an enemy blackmail leverage is out.
A certain amount of paranoia is desirable in security. The trick is not to be TOO paranoid.

troll