What a dilemma, I wont confuse by putting my four penn'orth in. But, I am moved to say that it looks like some people seem to have forgotten what the church and the service are there for.
Any sound checks, one two one two, should and could be done in an empty church. We are talking sound reinforcement here so any change in acoustic when the congregation fill the pews, as I hope they do, is not really significant.
Whoops my two penn'rth slipped out there!
A delicate situation though, I hope you find a peaceful solution.