The common formulation is that being intolerant of Intolerance is different, that it doesn't count. Taken as an abstract, I think that's true. Where it goes wrong is that this is hardly ever the case. The counter-intolerance expands rapidly to the people themselves and all their hateful tribesmen, and expands along another axis to include disagreements that can be called intolerance, up to and including positions that can be logically defended, but mind-reading suggests that the opponent holds the idea with bad motives.
Apparently there are Motive-O-Meters out there which can be purchased at a reasonable cost and take little or no training to operate. I can't find them on Amazon. Maybe certain organisations or institutions hand them out for free.