The proficiencies are getting removed but not the feat that is bootstrapped. All you can do is use the Helper.FtDisable tag to disable the feat. The feat will stay but will be grayed out and will not display on the 'Special' tab or get printed. It will still get shown on the "Feat" tab.
You need to get that "tags" are different than "Things/Picks". A feat that is bootstrapped is a Pick on the hero and CAN NOT BE REMOVED. You can disable the pick and then the script on the feat should not run but you can not actually remove the feat (ie pick).
So the code you found is correctly removing the "Tags" that control what weapons the monk can use. The feat in this case is sort of outdated an no longer used for new classes. This is so that when proficiencies are changed you don't have a feat hanging around that is no longer valid.
So change the tags to be what you need and simply do a
hero.child[XXXXX].assign[Helper.FtDisable] (change XXXX to be the unique ID of the feat) so that the feat does not get printed.