Well, yeah. If Choice A is, say, offensively racist (a group of sapient beings is predisposed to subservience) in context of the real world (this is a belief used to justify historical suffering), then no amount of Choice B's in-world justification (their god made them that way) will make it less so because the author had equal control over both and could have chosen to avoid the offensive Choice A by avoiding its causal Choice B.
But if the author's real-world intent is to call attention to and satirise the real-world belief, THAT will cast both choices in a different light.