Churches are exempt from many non-discrimination rules. They can exclude people who are not members of their faith, and may decide to kick someone out of the church should they divorce. The Salvation Army is anti-gay and actively lobbies against gay rights, as does the Mormon church.

If a company has the policy of not discriminating based on faith, creed, skin color, marital status, veteran status, etc. then it wouldn't be appropriate to support another organization which DOES so discriminate.

I have no idea if this is Google's reasoning, but it seems like perfectly ethical reasoning of why they may not want to extend non-profit discount to churches.

BTW, it isn't hard to set up a non-profit subsidiary. A church which wanted to could start one and use that to receive donations. There's some paperwork, but it isn't much - and most churches already have someone to manage their own paperwork. The new non-profit, of course, would be subject to non-discrimination laws.