Many of our polling places are in churches here, too. As far as I am aware, there has been very careful oversight regarding where in the church building voting activities can take place (e.g. the gym is OK, the sanctuary is NOT OK...) and it hasn't seemed to cause any discomfort. I agree it's a bit dodgy, though, but after all, we seem to have far more churches than schools. That this fact is part of the problem to begin with almost doesn't need saying!