Firstly, I'd look into laws in your local area and see if there's anything there to keep in mind. I recommend Transgender Rights | Lambda Legal to start

If your friend is okay with it, I'd report his mother as an abusive parent to the authorities. Does he feel like he needs his mom in his life? Does he want to connect with his mother? You'll need to sit and talk with him on these issues to be sure.

Secondly, I'm quite positive the authorities will side with you. If she kicked him out then decided you kidnapped him, she's obviously the one at fault here. Question if she really cares for her child's well being, or just wants to control him. I find a lot of abusive parents of transgender kids tend to just want the control of their child because they view their child as something that belongs to them.

What's really important is that your friend is safe both physically and mentally. I'm glad you're there for him to keep him safe And I hope everything works out okay. Be safe.