@olla,
If she doesn't want to date him, she has every right to turn him down. If she thinks he was asking her to his church for the purposes of asking her out (or to set that up), then she is certainly within her rights to say no.
For his part, he may be feeling a bit rejected or at least foolish.
I don't think it's such a hot idea for your friend to be pursuing him for a friendship. It seems like she wants to be able to reject him romantically yet maintain a cordial friendship. She kind of wants to have it both ways (get close to me, but not too close, or I'll push you away again), and that nearly never works out.
She should allow the guy to have a little dignity (and herself, I might add) and keep away for a while.
One thing about rejecting people, even if it is wholly justified, is that they sometimes get angry at us. And there are times when they don't want to be our friends anymore. It's a part of growing up and maturing to be able to accept the fact that not everyone is going to love us.