It doesn't make sense for there not to be contingency plans to take down the Justice League. Not only is mind control relatively routine, but almost all members of the League have rivals who have power sets similar (often borderline identical) to their own. Additionally, there's a multiverse of alternative versions of both individual superheroes and the Justice League itself, and some of them are outright evil. Even from a purely pragmatic, grounded perspective, the members of the League are - each of them, individually - an above-nuclear level threat. That threat is held in check purely by their own emotional and psychological stability, and their world contains some people who are pretty specialised in causing emotional and psychological damage.
It therefore also doesn't make sense for the contingency plans to be secret, or for the League to oppose their creation. Batman should tell the League what he's doing, and they should agree and enthusiastically help to formulate contingency plans to take themselves down in a variety of circumstances (ideally non-lethally).
Maybe those plans should also be somewhat protected. Like, a really good place to keep them would be on a properly secured computer. And not connected to a network. And also, on a space station controlled by the Justice League. And not, say, none of those things.
