The tax issue is a bit of a red herring.
If you tax churches you have to take every other charitable group - that includes groups you normally think of as charities and community groups such as sports clubs, garden circles and social clubs of the wrinkled and grey. Marae may also come under this category along with your local community hall.
Then again there are many multi-national corporations that manage to dodge tax legally.
Do political parties pay tax? I would like to know the answer to that. They are funded by donations just like churches after all.
Churches do pay GST and PAYE and ACC.
Pre Maori land settlements, the biggest land owner in New Zealand was the government
The second biggest was the Catholic Church.
The third was the Anglican church.
They lease land and derive revenue. Are you telling me they don't pay tax on this apart from GST?