Nick,
I would suggest that in addition to going back to church, that you do some reading. First- there are many books and articles on how to be a supportive, present, father. No matter what happens between you and your W, that little guy needs to feel that you love him unconditionally, and he needs to feel safe and validated. Second- you need to read about how to make a successful M relationship, because I feel that you really don't know what that would even look like. My recommendation on a book to start with is "Buyers, Renters and Freeloaders". You and your wife had a "renters" mentality in your R, which sets you up for a bad marriage. That's why I think this separation will be good for both of you. I think that you need to understand where you were, and what a good M is, before you can invite your W back into a loving relationship with you.

Quiet down and listen. Stop waiting to talk, you put your foot in your mouth when you do. Listen, listen, validate, listen some more. You think that you know your wife, but the truth is that you don't. She will tell you if you listen. BTW, if your wife complains to you, rejoice! It means that she sees hope (though it may not seem that way to you!). If you bully your wife with your words, she will retreat from you and stop any complaining and keep her interactions with you to a minimum. If you stop that behavior and start to listen and validate, she will slowly poke her head back out and complain. Do not defend yourself! Just listen and validate ("yes, I can see how much that must have hurt you" etc.).

If you stop making mistakes I think you have a VERY good chance of getting your wife back. Make sure to follow my advice on reading, though, or she will come back to a bad marriage and the next time she may leave for good.
-HS