In all truth I am suprised she is willing to let the baptism go ahead. There are Atheists like myself who probably wouldn’t kick off over it (I can pour water over a kids head myself in the name of Zeus if I really felt like it, I don’t think it’s going to do anything and I don’t expect anyone else doing it will have any lasting impact). But if she is an Anti-Theist as your post suggests (she believes religion is a toxic blight and should be destroyed) I’m actually very surprised she’s happy to let your husband do this.
If I may, do you know what kind of split there will be in time spent between your husband and the mother? 50:50, 40:60? On a more even or majority split you do hold the advantage in having what sounds like a more stable support base (“This is our happy family, we’re happy because we follow Jesus; look how lonely and angry mommy is, that’s because she doesn’t follow Jesus”). I’m not suggesting you say that to the poor kid, but that thought could well cross her mind with enough indoctrination and time spent on religious matters.
If it is the inverse however she might be more likely to come see you as the rather eccentric if mostly harmless relatives.
I think the biological mother is being remarkably compliant and supportive in view of her beliefs and I would be trying to include her in a positive light rather than trying to exclude her. Ultimately if she wanted she can put the brakes on this, keep it in mind. There are precedents for this in the legal system in several countries in the western world where courts have ruled Baptism must be withheld until the age of emancipation/majority.