Now the two of you have children together, you really talk out all these religious differences. I am a regular Christian attending the Alliance Church of Canada, and my husband is a Jehovah's Witness. We don't have children together, but we still have differences of opinion around the holidays. We talk about all these things and come to a compromise. The Jehovah's Witnesses similarly advise to show patience and love towards the non-Witness partner. Get a copy of "The Secret of Family Happiness" from the society. It has an entire section on the divided household.
If you want to be an involved husband and father, you need to work things out with your wife.
As for baptising the baby, I wouldn't worry about it. According to the Witness, it's not a true dedication to God. It won't make any difference to the child. If you are patient and a good example, in time your adult child may freely choose to get baptized in to the Jehovah's Witness faith.
On the other hand, if you fight with your wife on this issue, you will create a great rift between you and her. Not a good start as new parents.