I tell you what, I had a similar experience. I had been resisting my nature as a female in order to do what I thought would please God. At the time, I was under the misconception that being transsexual was an evil thing, and that I needed to struggle against it and pray that it would one day lose influence on my life. Naturally, this was not very helpful for either my mental condition or for my relationship with God.
One day, I became very concerned about our degrading relationship, and so I stepped out of blind obedience to what I thought was God's will and frankly discussed the matter with the Holy One. I spoke candidly on how I wanted to do what was right, and that I wanted to be a seed sown in good soil, but that I was having difficulty continuing to love a being who allowed me to suffer so. I got no reply to that prayer, not in any form. Things continued that way for quite a while afterward.
Then, after suffering a particularly painful bout of dysphoria, I again came to God to ask for the strength to resist my inner self. I didn't get very far into that prayer. I said "Father, I know being transsexual is a sin..." and was promptly cut off. I swear it to you all, before the saints and the holy trinity, that I heard a voice in my head immediately cut me off. It had one thing to say: "Why?" It never answered again vocally, but I knew in my heart from that moment forward that if I could not answer that question honestly and legitimately, I would have to abandon the notion that transsexuality was sinful. I also knew in my heart that I should not return to my previous sources for answers, and that I should rely exclusively on my own reasoning (which up until that point I had been taught to ignore). Don't ask how I knew what I knew, I simply did.
I pondered the matter long and hard. I tried desperately to reconcile this experience with my previous worldview. Surely there had to be some reason that I had been told that transsexuality was evil. There HAD to be something wrong with it. I never came up with any reason why it should be. Instead, I was led down the path of knowledge about those who had TAUGHT me that transsexuality was evil. They had lied to me, or they had not known of that which they spoke. I've never forgiven the organized church for that, and I don't know if I ever will. I was nearly driven to madness, and worse, to hatred of my creator, because of their foolishness.
At the time I remain a Christian, but I never allow any tenet, any premise, no matter who states it, to go untested. Nothing goes unquestioned. Even if it is claimed that Christ Himself said something, unless I can validate what is said as truth I will respond with skepticism. I will never surrender my ability to reason again, and no one will pull my strings and make me dance. I walk my own path now, and the only hand that I will allow to lead me is God's own.