I'm a little late to the thread but...
Wonko, you may not agree with the church/religion, but that doesn't mean you can't be supportive of her input on raising your child. This also means that she will have to do the same for you.
Have you thought about taking turns with your weekends? Find out the exact reasons for her wanting to have your child involved with church. Nuts-n-bolts reasons. Not specific stuff like "to praise Jesus", but more like "to have a moral foundation." Get a nice list from her and add the values, experiences and lessons that you want your child to learn. Use that list to create a family activity/day that reinforces what you and your wife want to pass-on to your child. Make it routine and every-other weekend alternating with church.
If you can't agree on a point-of-view, at least you can support each other.
Thorn and I have discussed it many times, though we are not quite in the same boat as you and your wife. Thorn wants our children to be raised in the Catholic church and it was discussed before we were married.
I know that I can raise my children to be good people, to do what is right and to make the right choices when they are sent out in to the world. I don't think that church is necessary for this. I do not know if I will be able to teach them spirituality or not. I do believe that my spirituality will show through my father-child relationship and they will learn through that. I don't condone or condemn religion (as a whole) but my pre-marriage experience with it wasn't the best (RLDS). I probably will not ever become Catholic, but I do go to mass with my wife, which isn't that often, and I am suppotive of raising our children as Catholic. Though I may not agree with everything that is done or said, it is a good morale foundation and a starting point for their relationship with themselves and god.
When they are older, they will have to choose what is best for them. Until then, it will be our job to give them the best that we have to offer in the way of experience and knowledge. If anything, being supportive of my wife and my wife being supportive of me will show them that love and understanding is important part of life.
I don't normally talk religion and I am by no means an expert, I hope that my point-of-view will help you do what is best for your family. After all, this is my first time as a husband/father and I'm just "wingin' it".