So... he's claiming that the only logically consistent position is that people are right about everything or wrong about everything?

He could have said something about homosexuality being a sin, or wrong, or against his values. He didn't. He said:

but they call the ones about putting to death the men who lay with men "ignorance" and "superstition."

Maybe strictly speaking this isn't an explicit call for murder, but it does seem implicit.

Incidentally, I would also be opposed to the murder of lepers, despite the fact that leprosy does objectively exist.

To make it absolutely clear, I am not bothered by the hypothesis that homosexuality is caused by pathogens, not that I think its particularly plausible. I just think that trying to fight the spread of a hypothetical non-lethal disease by murdering millions of people is ... words fail me.