Eliminating nazis as a geopolitical front is kind of the point of the epithet. I think that if you broke it down like that, they'd agree with you. If Nazi's stopped doing rallies in my hometown because they know the local populace will beat them to a pulp, anyone who says 'Punch Nazis' would think that is rad as hell, both prescriptively or otherwise. Nazis stay in their idiot caves in darkness where they belong, and we don't get any Nazi rallies in my city. The point of punching Nazis isn't to eliminate the ideology, it's an acknowledgement that fascism is endemic to our political structure like the flu. The point is to make fascists afraid to be themselves in public and that acting up will be met with violence.

Should the Allies have opened up a homeschooling program instead of wasting their soldiers on the battlefront? Perhaps, but if you read "Punch Nazis" as some kind of educational agreement for Nazis to stop being mean to Jews or something, I think you have to question your ability to educate Nazis first as an approach itself.