TG
You have a right to your own beliefs about this world. It's not necessary to take up a torch against anyone (discriminate or condemn).

I also doubt if God really cares if you see him as male or female. I'm pretty sure he'd put a dress on for you if it made you feel more comfortable, but then we're getting back into the other part of your question.
I'm not Catholic, but I don't see why it would be necessary for you to walk away from the church - especially if it gives you comfort. You can still take what you need on Sundays, and you don't have to be a hypocrite during the week like the others you've known.
No one should take away your relationship with God - not even religion.