Baptized Without Permission – OPP

On Other People's Problems, a man is upset that his ex took their son and had him baptized into a church he doesn't support. Can this be fixed?

Mike & Kate-
I have a 9 month old son. His mom and I were never married. We dated for about year before she got pregnant. We broke up before my son was born. We were able to work everything out in court and have 50/50 physical and parental custody. For the most part we get along. It's a learning process. Currently we're not getting along because I found out she had our son baptized into the Catholic Church on Easter Sunday. I am not Catholic and did not want out son to be baptized into the church and she knew this from day one. Since we couldn't agree on religion we agreed (or so I thought) to not baptize him into any church. When he was with her, he would go to her church and when he was with me, he would come with me to mine. We agreed when he got older he could decide what church he wanted to belong to. This was only a one time conversation but I thought we were on the same page.
Then I saw photos on Facebook of the baptism and lost my mind! According to her she couldn't go one knowing that if anything happen to our son, he would be stuck in limbo so she had to get him "covered" as she put it. I can't even put into words how much damage she has done to our son's eternal soul. Her church is an organization that goes against everything I believe. And now my son is forever tied to it.
I went back over our custody agreement and like an idiot, I didn't have anything put in there about religion. I don't know how to make this right. You can't undo a religious ceremony, can you? Should I talk to her church and let them know I'm not in support of this? That she did this behind my back? My family says I should just have my son baptized in my church. I worry he has already been damaged by the first baptism.
Has anyone ever gone through this? I find this unforgivable but know that I need to forgive her in order to raise our son. It's just such a sign of disrespect.

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