There are already denominations that fully accept gay people, so it can't be that.
I think Atheists leave Christianity because of hard attitudes amongst the more Fundamentalist groups, the threat of Hell if the "rules" are not followed, and the lack of proof of God's existence that is the main theme in the lives of MOST human beings.
Because we are not constantly wishing most for God's presence, because are lives are busy and difficult and it is important to spend 99% of the day being sharp in the modern world, we don't find the time to seek God. So of course, if you don't knock on that door, it will not be "opened unto you."
Only those who make finding God the chief focus of their everyday life will find Him.
So Atheists, who live very much in the workaday world, do not find the proof they seek.
I believe in Reincarnation, and I feel quite sure that in some life some time, the circumstances will be right and the people who found Atheism to be right for them in the 21st Century will find spirituality right for them in another place and another time. I see God as being endlessly patient, and not at all angry with Atheists.