I don't think simply having a story where Punisher denounces alt-right people who use his symbol would do it, since I doubt most of those people read comic books, but maybe a combination of two of those ideas: have the Punisher realize his symbol has been hijacked, strongly denounce it, realize it's gone too far to stop, and change his symbol, never to use the old one again (and also have Marvel switch to the new one for all of their merchandise). Even with all of that, it's probably not a good idea for the Punisher to be one of Marvel's top properties, always with an ongoing. Treat him like Taskmaster or Black Ant, villains with a capacity for good who once in a while get a miniseries, but aren't considered forefront characters.