I've been aware of the name Kirk as a first name longer than as a surname, so it's not surnamy to me. It's a lot like Dirk - middle aged, but bold and bright enough to be used for a boy born now. The father of the family across the street from me is a Kirk, and the name suits him really well -- he's a laid back guy but high-energy, planting his yard in the rain and stuff.
I don't get why it would bother you for religious reasons. The surname probably just referred to someone living near a church.