The influx of people interesting in fighting Scientology had little negative effect on the morals/behavior of the people hanging out on /b/. I think you're right that the community changed, but not for the worse in terms that non-/b/tards would recognize.

Actual /b/tards didn't like all the unsocialized newcomers arriving and parroting memes that they didn't understand ad nauseam. They also didn't like the moral crusading aspect of the newcomers. Neither of these behaviors is a negative change in the community from an outsider's perspective, but it was from an insider's perspective.

The Scientology campaign didn't change the (sometimes satirical) celebration of racism, porn, fascism, child porn, misogyny, and so on--all that pre-existed the influx of new people interested in fighting Scientology. If anything, the new people watered down the sociopathic culture of /b/.