In conservative evangelical churches I do believe they would be.
Same.
"Deny" isn't fair. "Struggle" perhaps. Holding their behavior wrong - yes.
Being intersexed, transgender or gender non-conforming isn't "wrong behavior", it's being the person God made you as, even if you're very much in the minority. In fact the idea that it is "wrong" is suggesting that God is wrong, an attack on the inerrancy of God. That to me is a blasphemous position.