Did you hear any policy or theory of homosexuality in the organization?
Hubbard asserted that homosexuality was always associated with suppressive persons. Calling someone an SP (Suppressive person) is just about the worst term available in the entire scientology lexicon.
They are to be shunned, avoided, destroyed, etc.
That being said, the first person I personally knew who died of AIDS was a scientology staff member (this was before AIDS had even been identified as a disease).
It's also rumored that Hubbard's gate swung both ways...
Would Miscavige and company destroy Travolta to protect the church? In a heartbeat, with no more hesitation than you or I would have in crushing a cockroach.
Beyond that: would a "clear" actually engage in homosexual behavior?
Theoretically, no. In practice, achieving the state of clear does not change brain wiring or body chemistry. I don't have many connections in the church these days, so I don't personally know any queer clears...
I agree with your earlier point that the internet is helping to expose the fallacies of exploitative pseudo-religions, especially by posting the so-called secret documents. Once the hidden secrets of the various false religions get widely read, especially the warrior cult in the mid-east, there may be hope for humankind.