Not all pagan churches. For one reason or another, the Zoroastrians got a pass.
Maybe because they were too big to smash (I honestly have no idea how many were left from the crushing of the Persian Empire by Alexander followed by expansion+evangelism by the Romans & Greeks). Maybe because Muhammad figured they were one of the good ones. Maybe because the precepts of Zoroastrianism are not altogether different from/compatible with those of Islam & Arabian myths. Your guess is as good as mine.
But the fact itself is indisputable.
Then again, I mean, the early Romans (and to some extent the early Greeks) were pretty unique in their synchretistic approach to religion and imperialism - and even that would change radically when both halves of the Empire made Christianism mandatory. You can’t synchretize with a One True God anyway. Jus’ dun’ work. You can appropriate, but that’s a different concept.
Anyway, the point is : everywhere else, and every other culture I’ve studied in any kind of depth, the first thing they did upon conquering some new territory was wreck every sacred site and, if possible, annihilate the local history. Makes pacifying the place much easier, as the next generations will have fuck all to go by and identify themselves with besides “part of the X Empire, as we’ve always been”.
Hell, the Christians did so too, to more people, and until much later - what do you think the crusades against heresy were about ? Efforts in Cathar anthropology and preservation that went overboard ? 
The Teutonic knights hardly fucked about in Lithuania, Poland… real unseemly shit went down there, yo. Nor did the reconquistadors in Spain mess about, *or *the just_conquistadors in the Americas - a fact that to this day makes historians weep, because they/we sure could have done with a codex or two hundred to figure out what the hell was going on out there before Columbus - instead most of the history we’ve gathered on that part of the world is based on guessing what this or that stonework could possibly have meant, dreaming up rationales for this or that geegaw and collating half-remembered folk tales still extant among the great great great great great grandchildren. Same viz how Native American tribes worked - there, too, Europeans did a splendid job deliberately wiping out the oral histories, eroding tribal cultures and using the settlements & artifacts for firewood. Much effort was expended wiping any tribal and African culture from slaves as well.
It’s about order and control, and it’s just what you do if you have an ounce of good sense (and you’re interested in conquering places, of course). When you don’t bother doing that, well… how’s Palestine these days ? 
None of this makes Muhammed morally right or justified, of course - I’m not in any position to debate morality, being an apathetic misanthrope, and philosophy always felt a lot like wanking to me anyway :). But it provides some IMO needed historical and contextual perspective.