This is a very sensitive topic to me as my W has seemingly drawn closer to "religion" as she is going to church where her last OM goes. He is very active in his church and, according to her, has expressed a lot of guilt over what has happened. He wasn't aware that she was married when he got involved with her and he also was slipping away from the church at the time.
She came to me once and said that God told her to leave me and the marriage.
My point is that I have a hard time believing that God would sanction someone leaving a marriage while at the same time finding Him. If she is really seeking Him; I have to believe that He would place upon her heart the need to come back to her marriage.
At the same time I understand your confusion. God works in HIS own way; even so, I highly doubt that he would want her to leave a marriage just to get close to him. But then again we don't know. Maybe God wants YOU to be free and HE wants YOU closer to him. I know that my experience has brought me closer to him.
I've prayed the same prayer that maybe this is what will lead her to Christ. I just question the means. In my W, I see a selfish bent to her new found "religion."