Wow, you have given us quite a bit to think about. And I am glad you have given your life to the Lord. I don't think you should feel shame - I think you are grieving many losses.
One thing that straight spouses of gay bi and trans people find is that they lose who they are with the involvement of whatever the GLBT persons issues are. With spouses of trans, the loss of identity and relationship trust is enormous. So when your wife left you - it was out of desperation that she needed to be a normal functional female mother and human being. She cannot continue to be mated for life with someone who started out male, then was transitioning to female, and now is not sure that was a good idea (sounds like you want to stop the process now). And really, it is difficult to reconcile with someone who could even consider such a thing. The trust issues are huge.
In my support group, I have encountered spouses of GLBT people who deal with husbands and wives who suddenly decide oops, no, that's not me after all honey, I'm good now, come back. Sometimes they do, but often not for long. Life is much better when you are free of a spouses drama, and only have to focus on your own - and straight spouses of GLBT people often have to deal with quite a bit of drama once the sexuality is disclosed or discovered.
Please understand that if you are stopping your transition, it may not get your wife and son back. Being a Christian, giving your life to Christ may not get your wife back. All you can do is move forward with rebuilding whatever relationship is possible with them.
I strongly encourage your wife to get in touch with the straight spouse network (
www.straightspouse.org). This is a nonsectarian support group for the straight spouse, and there are wives of transsexuals and transvestites among those who attend the support groups either in person or online. Whether this does you any good, I can guarantee you it will help your wife because she will know she is not alone in her feelings and can talk to someone who really understands. It's a non profit, and outreach is free. Everything is confidential, and there is an emphasis on building bridges and having the best possible communication going forward. Just about every wife of a transsexual or transvestite that I have known leaves the marriage. There is a forum on the website which is public, and that may be of some benefit to you for advice how to remain connected to your son. The online support for straight spouses is not public, it is confidential.
As the straight ex wife of a very closeted gay man, I found this group to be a lifesaver. No one wanted to listen to me and I really needed to talk out the experience, which was ongoing.
If you let her know about the resource of a support group for her, she may well appreciate it, because it shows that you are focusing on her and her wellbeing, not on who you are, but on who she is and what she needs - no matter the outcome for you.
I'm praying for all of you.