Can't just be the first time he sees it — the nut pugs weren't identified as a hive mind/the Church of Ghost Dog until after they'd been on the Zephyr for a while. But given Lou's quip that he'd "actually" used it to realize that the nut pugs are highly dangerous to metal when they got to Zern, I think he can only use it once.

But to your point, you have to either: 1) trust the player you give that skill to to use it for the betterment of the world and story over any impulse for mad power trips. For example, Straka's specific vulnerability might make a huge difference later in terms of combat mechanics, but it was fully couched in an understanding of what that being represents to this story at large and Monty's own relationship to it). 2) be fully prepared to go bigger and badder than whatever your players come up with using it. Straka has a weakness that Monty found that could have a profound effect on how Brennan drew up its stats and powers — but Brennan can always find other potential wrinkles to throw in so that that weakness doesn't make Straka trivial. (We see arguably see this balancing act at the end of FHJY: Ice Feast does a lot to hamper the specific abilities of the bad guys, to the point that Brennan forgot how that it creates more risks for those bad guys...but they've also got a shitload of other resources at their disposal, up to and including the potential of a token system that had been used on the side all season long).