They can be especially effective disrupting a third party religion in an area where the prophets religion is not strong. This can allow your religion to cross a critical gap, where it then spreads organically.
For example, if 12 cities influenced only each other, and religion A is leading religion B (yours) 8 to 4, a GP from religion C with two spreads could make it 6 to 4 to 2 when used on A's cities. If one other city converts to B with a missionary you have a fair fight, and if you get two the group is probably yours.
Obviously this can result in a diplomatic hit, but it is very useful if you're trying to become the dominant religion. Not so much if religion is just a side gig.