it could be in your head, like you're a witch so you think something might happen when you enter a church, so your mind tells your body to act differently.
mind you, i have a friend or two that swears they feel different in or near churches. granted, those people like to overreact and be the center of attention, so i don't trust them too much. i've been in church a few times after converting [my family is christian] the last time i went, i felt uneasy, but no time before that.
if you feel bad, then just don't go, it's most likely in your head, but if you don't feel good, you should avoid it. if you aren't being forced to go, then don't, if you need to walk past it, cross the street, but nothings going to happen to you.