You can just add another field of the type boolean, if checked, then pin it to the home page. All the show on homepage does is determine to show it on the home page by reading in that boolean, if true, then it shows, if false then it doesn't. After you add that field, then go to your where clause and add your condition.
Usually best practice is to clone the code files, but with built in document types, usually you are ok to add your own fields. I usually won't delete fields though, just to be on the safe side. Also, cloning that document type isn't a large effort at all by any means or even creating your own. If you have the time, why not go ahead and do that, then you can protect yourself against future upgrades.