Honestly I like to imagine they weren't even really mind control per se, but basically prevented people from just ignoring or deflecting his preaching, and have to hold it to the same standards as their current beliefs. If so the people who would have joined his flock would be people who had less cogent beliefs before, who ended up realizing his stuff made more sense. Cocomittantly, someone who had a better meme would be immune to everything that contradicts it, besides maybe having to debunk it manually. As well, presumably if someone came along with a better idea it may be able to dislodge his words, though presumably at a similar disadvantage to what he had before himself.
Given that the wishes don't seem to twist in that sort of way, and I'd like to imagine young Kyouko didn't want everyone to obey her dad unquestioningly, just genuinely listen to what he had to say. It's possible she may herself still have his words rattling in her head, but that once we can poke holes in it they may lose their sort of grip.
That definitely doesn't fit with my interpretation of Kyoko's story.
As you say, wishes go by intent, not literal genie words. Kyoko's intent was not that people would listen to her father, but that they would listen and believe what he was telling them was true. Sure, she wanted that, in part, because she already believed it was true. But it was an explicit wish to violate free will, since the people who freely chose to leave the church when they didn't like what Pastor Sakura was preaching were the problem Kyoko saw her wish as solving.
I know we've got strong feelings about mind control that might tempt us to say what Kyoko did must've been something less invasive, less of a violation of another's being, because we like Kyoko and sympathize with her plight. To whitewash what she did in order to not have to reconcile the fact that we rightly consider Kyoko as a victim in what happened with our feeling that violating someone's mind is unforgivable.
In a sense, I imagine this is what Pastor Sakura might have been feeling when he realized that he hadn't just finally found a receptive audience for his sermons. Free Will is placed on a very high pedistal in common Christian apologetics due to the idea that it must be the highest possible good if God chooses not to violate it even when people use it to enact the most horrific evils upon their fellow man.
I think Kyoko did, in fact, do a bad thing. I don't think Kyoko is unforgivable for doing it, and I do think there were a lot of mitigating circumstances which make her less culpable for the decision she made. But I do think she did wrong, violated other people on a deep, fundamental level. She didn't mean for that to be what she was doing, but I think it's more that she didn't think through the implications.
Wishes aren't literal genies, but they aren't benevolent genies either, carefully arranging things so we'll get what we really want instead of what we intended when we asked for it.
And I don't know how I missed something so obvious, but Kyoko wished people would listen to her father. And her father blamed her for his murder/suicide. It had seemed like such normal survivor's guilt and hindsight showing her where she went wrong that she tried to pass on to Sayaka. It somehow never occurred to me that her inability to forgive herself might not be entirely natural.