answer.... 1) Ignore the email completely and see what happens.
She is telling you that she thought this over deeply. She went to church and was convicted by the message at church. That message was that she wasn't living in harmony with her beliefs. She then told herself that she either had to stay married and dump OM or get divorced and be with OM.
Her mind (led by her feelings) then told her she wanted OM. She has decided that she thinks she will lose the guilt by divorcing you. (possibly not true)....
She doesn't want to hurt you because she does care for you, but she had let go when you left last year and doesn't feel the same way that she used to feel about you romantically.
In the meantime, you come back and now want her and will be the husband she wanted all along. This initially mixed her up. With your coming back and causing arguments and problems now with wanting her back, whining about the kids being with her when OM is around and yada yada yada, has caused her to lose the fact that she WAS becoming HAPPY without you. She has now realized that she has lost focus of that happiness she was starting to feel without you and now is back to UNHAPPINESS and inner turmoil..(which she is now realizing is your biggest asset.)(causing disruption and turmoil to her life leading to UNHAPPINESS and questioning and issues and problems)(instead of peace of mind and joy and excitement and happiness)
She now has decided to focus back on being happy and taking care of herself and has realized that you are bringing that down again. She is hoping that you understand that YOU are where she was last year and that you will find out the same things she has, which is that "this is for the best" and that maybe you can be friends and raise the kids togther, but that she is choosing the OM at this point.
I don't see a hidden agenda in this email. She is trying to tell you without hurting you (typical woman who beats around the bush to avoid hurting someone)more.... She HAS decided which direction she is taking and why...
I would ignore it. That doesn't mean you don't get the messsage that she was trying to send.