"I'm pro-vaccine, but I want to let my children make their own minds up when they're old enough." This is the kind of thing you never expect, and do not even want, to hear a parent say. Part of being a good parent is not simply letting your children make up their own minds about everything, but making their minds up for them until they are ready. Children don't know what's good for them, so we should never let them just make up their own minds.
But when it comes to Christianity, apparently, it's totally logical not to teach our kids about Christ, they'll just come to their own conclusions later on in life. But if you know Jesus, the most loving thing you can do is make sure your children do too. It's not even about "letting" them make their own minds up. Really, you don't have a choice about whether or not they make up their own minds. It's not like you can be 100 years old, and your 80 year old son can say to you "Mommy, maybe we don't have to go to church today?" "No, Timmy, we have to go to church, or you don't get an ice cream later."
You don't get a choice about what your children believe or do. The truth is, kids are always going to rebel, they're always going to be independent, and they're always going to make choices that one or both parents disapprove of. That's just reality. But while you can't choose whether or not your children remain in the faith, you can choose whether or not to raise them in it. There may come a time in a child's life when he doesn't want to read the Bible anymore, but that doesn't mean you shouldn't encourage him to do so in his early years. There may come a time in a child's life when she decides to skip church. It's unfortunate, but as long as you have full custody, bring her along with you. If a child makes a bad choice, let that bad choice be solely upon their own heads, not because you decided to let them make it without instruction. Let them make their minds up when they're ready, but equip them with a Godly mind until then.