They stopped very much short of making a legitimate criticism in a few ways

1. The Project at Eden's Gate cult isn't racist, like at all, the folks at the top are all lily white. The game never makes a point of it, despite the fact that the actual cult membership is fairly diverse, which leads to...

2. They literally brainwash everyone with drugs. This is the implication behind why they're so numerous, they're just drugging people so they're suggestible and then indoctrinate them while pumping them full of their magic flower dust. There's no mention of them taking advantage of the desperate or the foolish or anything, they just kind of drug everyone and everything, including you, the player.

3. They're ultimately proven right in predicting that the end-times were close. The developers basically try to pull a big "fuck you" in the vein of Far Cry 4 by suggesting that if you just left the cult alone, everything would have been fine. Yeah, sure. Despite the fact that they were already killing and drugging everyone in the fucking county, leaving them alone was the best option. Even in that circumstance, NUCLEAR WAR BREAKS OUT AND EVERYTHING BURNS ANYWAY

It's really toothless and doesn't actually have much to say aside from "You are bad for wanting to do something about them"