Okay, folks, here's the deal.
For those that weren't around for/don't remember Utsuho Quest, Koishi and the goddesses were pretty adamant they were in the right about creating Gensokyo Isle, because they had taken pains to make sure everyone's life was 'better'. We tried arguing the morals of autonomy and how people should have been allowed to choose the 'better' life, and it never really got through (and perhaps isn't the morally superior position even though we took it). We're not going to get that to work three years later, particularly as a relatively unrelated party, so we shouldn't bother trying.
HOWEVER
There were two objectively wrong things with what they did:
* The SCP Foundation is now alerted to Gensokyo's presence, and who knows how they've spent the last few years. Sadly, despite our being one of their security guards, we obviously don't remember nearly enough about what happened to try to use this in Utsuho's favor/get Koishi to rethink things. It's also not really something they could have anticipated.
* Dragging Gensokyo out into the middle of the Pacific Ocean cut it off from Higan, stranding the souls of departed and recreating the Kaeidzuka Incident except with no slacker shinigami to kick in the rear to fix everything. This Youmu would know, both the seriousness of cutting Gensokyo off from Higan and what gobs of weird flowers would signify. (It's also something Kanako, at least, really should have planned for, but that's neither here nor there.)
Getting to that second one, I believe, is the key to getting Koishi to reconsider. It doesn't absolve Utsuho of what she did, but it does shake the foundation of "what I did was right" that Koishi has been sitting on all this time. We need to get one of them to let it slip that the islanding of Gensokyo is what happened, though, while playing as if we don't know that's important.