They never changed the lore, players just misunderstood what the Arathi are.
The impression some players had was that the Arathi had arrived from the Eastern Kingdom 15 years ago, and that there was some mystery as to how they arrived from the past or whatever.
What the lore was, and which some players got confused by, is that the Hallowfall expedition arrived 15 years ago from the Arathi empire, which is somewhere we have not yet seen.
Adn sure, the giant cathedral is a bit of a stretch. But we know that they were more or less at peace until Sargeras' sword hit, and that they had plenty of trade with the Earthen. It's not unthinkable that being such a zealous people, that they focused on making the Priory with the help of the Earthen to get it up quickly.
Also, they don't really have their own culture beyond what is reasonable. They are zealous, like what the Arathi empire at large likely is. And they were all part of an expeditionary fleet mostly comprised of military personnel.
The biggest difference is them not being overtly xenophobic, which is fairly easily explained by years of trade with the earthen combined with their need to be pragmatic against the Kobyss and Nerubians.