Hi Hooah, do you think your wife would be open to both of you preceding statements to your kids with, "I believe"?
e.g. "I believe that God doesn't exist."
"I believe that God does exist and that Jesus is his son."
"Mom and I don't agree on these things but that's OK, everybody's different."
So instead of indoctrinating them, you are presenting your points of view to them and allowing them to eventually decide for themselves what they want to believe in.
As others here have said, the fear of hell might get in the way of this, but it's a possibility if she can be somewhat open-minded.
Good luck, sounds like a difficult situation.