We're in a similar situation too (or were 3 years ago). Atheist parents sending our children to a church-y school with no real alternative school; so much so that we seriously considered home educating as PP have suggested. In the end we decided to go in with an open mind and give it a try.
DD is in year 2 now and DS in reception. I've been to a lot of the assemblies / things that parents can attend and am generally happy with what goes on. It is more religious than I ideally like ; lots of references to god and Jesus, lots of bible stories and songs etc. It was a bit uncomfortable at first because it's not stuff I'm familiar with, however when i looked beyond the "god talk" the messages align with very general values of friendship, kindness, forgiveness, respect and the like, things anyone from any background would be able to relate to and think of as positive attributes.
There's a difference between promoting Christian values and promoting Christianity (or insert religion of choice in here). The school are very conscious that they do that; most of the outside speakers are from various local churches and usually say something along the lines of "I believe" rather than "this is true" and "I'm going to say a prayer now, join in if you want to or just think about what we've been talking about"
DC come home with lots of questions which we answer as honestly as we can. We also bat some questions back to school and the school encourage challenging questions so it's all good. They're definitely not trying to convert non-believers, and mostly don't assume all the kids are from Christian families, although occasionally someone will say things like "we believe..." until a child very rapidly pipes up with "I don't!" or "so and so doesn't!" and there is an apology / correction.
Its a very laid back, informal school though so I can imagine that it potentially wouldn't be as good natured in another setting.
I don't think religion has a place in schools at all (apart from studying it in the broadest sense) and that families and communities should take care of that from within, so ideally my children could go to a school that had no emphasis on any religion. However, the school our DC go to is a really nice, caring place that's excellent at pastoral care and I think that's come about by their focus on their values ( of course, as an atheist I don't think people need a religion to have values) so it's worked out fine for us so far.
Get to know the school OP and see what you think. 