His religious beliefs are a choice. People's sexuality isn't. And if his religious beliefs frame LGBT people in a negative light then they're inherently malignant. Being gay isn't.
Not affording X the same level of respect as Y is only hypocricy if X deserves the same level of respect as Y. And in this case it doesn't.
People need to be tolerant of his religious beliefs, as long as they don't actively impinge on other people. But being tolerant doesn't mean you can't criticise him, criticise his beliefs, criticise his religion, think his club should disassociate themselves from his position or think his club should reconsider whether he's the man to represent them as captain.
Religion is as much a choice as having a belief that the world is round is a choice. Belief isn’t a choice - it is a conviction. Can you choose to be a Muslim? Nice try justifying discrimination against religious groups though while standing on your high horse.
Will you extend this to the Jewish community who hold that same beliefs - genuinely interested?
Also, not having a choice in something doesn’t make it ok. Just as society has reasons to be morally against pedophilia and incest, Muslims have reasons to be morally against homosexuality. The key word here being morally.
And before your heads explode, being morally against someone acting in a certain way doesn’t mean you discriminate against them in the public sphere, just as Muslims are morally against drinking alcohol or sex outside marriage but can still hold good relationships with people who partake in said actions. Or are we going to discriminate against religious people who hold these views too?
Unless of course we are turning into a society that polices thought, I’d be careful with your line of reasoning.