Well ... Okay, put it like this. When information is presented in the narration by the viewpoint character, readers tend to accept it as true, unless the context or their own prior knowledge makes it clear that the character is wrong. The only suggestion to the that she is wrong 1. was presented outside the story after the fact, and 2. as its primary support, it uses a character who is widely disliked by the fandom and is generally seen as a hax Mary Sue for, among other things, doing precisely that kind of thing. (For that matter, I imagine ZUN wanted her to seen as a "morally-messed-up villain," and kind of overplayed his hand.)
And even if you do accept it as a legitimate tactic, Yorihime still had a lot more justification for what she was doing, in that she was fighting off a percieved invasion. In this story, Koishi basically just invaded Gengetsu's home dimension, forced her into a duel in which Gengetsu had nothing to gain and Koishi had nothing to lose, and beat her up and kidnapped her, all this for no reason except "cuz I wanna." I don't feel like there's room to view her character in a positive light, even if you shoehorn in something like "oh, she doesn't really know any better/mean anything by it."
But okay. It's still early in the story; I'll wait to see how it turns out.
