We are Catholic and my sons attend Catholic school. For my youngest, we enrolled him in a Lutheran church run program that was wonderful. While the philosophical differences between Lutherans and Catholics are fairly significant, we felt completely comfortable there and he had a wonderful experience. He learned about Gandi and China and community service and a bunch of other stuff that I was surprised by. He also learned to wash his hand and play nice...it is, after all, preschool. They did pray before meals and they sang a hymn.
I agree with the folks about the use of "brainwashing." Being non-religious is your family value and there is nothing wrong with that; just as your choice to be non-religious should be respected, so should the choices/beliefs of the individuals who work at the church run preschool, many of whom probably volunteer their services (which is part of their religious beliefs ) and it is this volunteer work that would make it affordable to you. Does this clarify why some might be upset by your use of "brainwashing?'
Before my current job I worked in gifted education at an Ivy League university. Unless your son is so highly gifted that he cannot function in a normal preschool environment (which is possible in some cases of highly gifted children) then you do not need to be worried about the curriculum and pushing him. Seriously. Let him be a child. If he IS that highly gifted, then he may be consider "special ed" (which by the way is supposed to serve both the highly gifted and the learning delayed) and that is a whole different issue. You would need to get him evaluated and then access resources through the school district.
BTW, part of the reason I left my last job was the difficulty in working with the parents of gifted children. It is very hard to find the balance between advocating for your child and becoming a helicopter parent who achieves a certain level of status due to her child's accomplishments. I am not saying you are doing this, just that it is something I have seen and I could tell horror stories of what helicopter parenting does to highly gifted kids. I happen to be the mother of a highly gifted son as well, so I do know what it can be like to get the questions (especially in the toddlers years) and I knew from my work that the best response was deflection. In other words, I found something positive to say about their child so that the focus would not be on my son. I am also careful to reward my son for his effort and not his grades or easy successes. I could go on and on about gifted kids, but I won't. I just wanted to give you a few ideas. He sounds like a lovely boy and I am sure you will find a great place for him that reflects your family's values.