Most Helpful Girl
of course they won't accept you. They don't accept anyone different than themselves, that's just something you'll have to live with when you deal with people and a religion and culture that is ancient and backwards and brainwashed and is allergic to being progressive and letting people choose their own path in life and being able to be themselves.
Obviously being Atheist and Trans you stick out like a sore thumb in that culture, but at least you are not a puppet like they are and can think for yourself and make your own decisions and conclusions. You can hope for the best, you can't expect them to accept you, cause that's not part of their culture. I wish you lots of luck.3
Most Helpful Guy
Given how you think they might react, I think this is one of those of those unfortunate circumstances where you should hold off on telling until you are absolutely ready to cut ties if need be. Rather, if they decide to give you the boot, you should be independent and stable not to be screwed over by it.
If you tell them now, there is a chance, given your location and situation, a strong adverse reaction happens. The bad reaction may not be possible to avoid once started, so my advice is to avoid it until the time is right.
Once you are set in life and have found your way, then tell your parents. (Or hide it for life, and don't explicitly state it, but don't keep it a secret. I suggest the former way as it may be a burden to live expectations you don't want to live under.)1