The usual way to handle such cases is "reflective equilibrium". In a simple variant of the Mere Addition Paradox we have three intuitive premises: A+ is not worse than A, B- is not worse than A+, B is not worse than B-; one intuitive inference rule (transitivity of not-worse-than); and one counterintuitive conclusion. For those who feel the pull of that typical pattern of intuitions, you just have to decide which (at least) one of those intuitions to reject. (Trying to explain each one away often helps.) Other things being equal, if we wind up rejecting exactly one intuition, we will be "integral thinkers" N/(N+1) of the time, where N is the number of premises+rules that leads to the counterintuitive conclusion.

The "integral vs differential" framework is useful for identifying cognitive habits or biases. But once we lay it all out as a choice between rejecting statements or inference rules, the terrain looks different.