We are also Unitarian. I know a number of families from our church who've chose to send their children to various religiously affiliated schools in the area. In many cases, they've made the choice for academic reasons. We are in a urban, liberal area so the schools they've chose seem welcoming. The private school we were most seriously looking at our is our local Quaker school (Friends), which is especially known to be welcoming to everyone and the "chapel" they do is very simple.

I personally had a very bad elementary school experience at a small, very old fashioned Catholic school (I was raised Catholic), so I personally refused to even tour them when we were looking at schools. That being said, I know several families that had to pull out of local Catholic schools for academic reasons. It just depends on the school!

Good luck!