Starsector 0.97a is out! (02/02/24); New blog post: Simulator Enhancements (03/13/24)
You could just edit data/config/settings.json and set "minInterestForPatherCells" to some high value, say 1000 or so. That should (I believe? never actually tried it) remove Luddic Path *cells* from all colonies after a few days, though the Luddic Path itself will, of course, remain.
I think the real solution is to make the smugglers for Pather cells actually the Luddic Path faction, instead of them sneaking through willy-nilly as "independents".