Sam, you are quoting the exception as the rule. Surely, we weed out Minhagei Shtus, but we are very reluctant to label one as such. And ultimately, it is this checking process that givess Minhag its power.
An organism is kept alive on its own. Once in a while outside intervention is necesssary, but that is the exception, not the rule. Usually Minhagei Shtus don’t kick off in the first place. In the event that it did, and it contradicts the Halacha, we check it with what is written and weed out those few.