I've come to realize that children are much smarter than many give them credit. The chances of them becoming a JW are very low since you are behind the scenes showing them the truth about the organization. Dave (AA) and I had these concerns too when we first came out. We were putting down rules and saying to my parents what the could or could not say. But, it wasn't working out. JW's are in the "saving" mode and feel like they need to save everyone...including their grandkids. But after thinking about it, Dave and I realized that we have them 99% of the time. So when they get to grandma's house, if she wants to try to teach about the "paradise"...that's fine. And if grandpa wants to pray to there god Jehovah, that's fine also. Because we can then show our kids the hidden truths about the org.
As far as becoming Atheist...or into other religion. IMHO, let them explore. If you start "forcing" them your religion...or any religions, they'll only rebel and become what you might not want them to just to spite you.