The solution to this problem is exceedingly simple: Herbicide. Zetsu seems to be some kind of a plant, so he should be much weaker to many common herbicides than regular folks. Of course they could also do it the more traditional but boring way of clearing everbody through their friends who should be able to ask the right questions. But that would still leave a margin of error, like two Zetsus clearing each other. So, my suggestion surely is Roundup.