Arguably not a bug, but a "feature." If you truly eliminate a civ (i.e., no more cities -- none at all), then this should not be a concern unless another civ liberates one of his cities and revives him. If, however, you have conquered his capital and all but one of his cities, leaving him with one lonely backwater city (perhaps in an effort to avoid warmonger penalties for eliminating a civ), then, yes, he can eventually spawn a GP and respread his religion.
This is particularly bothersome when your religion has some great faith-giving beliefs and he uses your religion's beliefs to generate enough faith to spawn a GP or two.
On the 3 spreads with a GP point, you can't create a holy site if the GP has fewer than 4 spreads left. So, if you manually buy (post-Industrial) a GP in your Great Mosque city, it will have 5 spreads; you can use one spread and still plant a holy site. Also, if you are playing Sweden, you can gift a GP with only one remaining spread to a CS to get 90 influence -- which may be more valuable than using that last spread mission on another random city.
Yeah but...His faith is non existent anymore and it should work the same way purchasing works i.e. if you buy a prophet from an Islamic city it will be an Islamic prophet, even if your religion in the rest of the empire is Shinto.
And since they are so much concerned about having lost their won faith why dont they convert their own cities first?
I honestly think its a bug/programming oversight. I can see the benefits of capturing 'rogue' prophets but sometimes you just see notification because you didn't look at that particular place and you facepalm when you realize what happened!