What does this have to do with religion? Secular ideologies killed about a two hundred million people in last century alone and nearly destroyed all of civilization. Secular Totalitarians were putting people in gas chambers and gulags by the 10s of millions 'In The Name Of Whatever' (and of course, about 1/2 of those secular ideologies were specifically anti-religious). If you look at a map of Europe, you can see the…
I think the finding of this study is suggesting religious persecution is bad for for a community, not religion itself. It would likely see all the persecution you mention as harmful, just not part of this study.
If the study was titled 'Long-Term Effects of the Spanish Inquisition' - that would be fine, but they are more broadly applying their conclusions without evidence.