No, and I don't think that's a reasonable policy. The only fees we waive are for county projects. I would think if you waived them for churches, you'd need to waive them for all non-profits? Just because they're a church doesn't mean that you don't incur costs to review and approve their plans or requests. I don't see how their religious affiliation changes that in any way.
We just ran into this with a Unitarian church (of all things.) They had a lawyer write to us that our third party review and inspection fees were taxes and they are exempt. The real problem there is that their consultant is one of the ones that we always have issues with. The third party consultant ended up being willing to waive half their fees in the interest of world peace.
No waiving fees on religious grounds unless your willing to waive it for every religion and possibly all the non profits. We waive taxes for any non profit that asks and fills out the right paperwork. It gets churches out of the tax rolls along with fraternal orders and the hospital (non profit my ass).
We do waive fees for buildings destroyed by some disaster like tornadoes (did one last month) and fires. Bulldozers are not considered a disaster and yes I know tornadoes sometimes do a lot of improvement to the area.
Thanks for the replies. We have a lot of non profits and churches, waiving all fees concern me. Especially that this isn't just a church, it's a church with a daycare and all the other community programs. Much more intense than a church.