Yeah, Judge shouldn't be anywhere near the QBs. I'll be pretty disheartened if he stays in that role next season. There are other places I think the assistant coaching is lacking, too. They could afford to reevaluate their staff and see about bringing in external coaches to complement and expand upon what they're doing.
As far as the offensive play-calling, Patricia has been pretty good this season. I doubt he's becoming an entirely different coordinator under Zappe, which would seem to suggest he's intentionally sabotaging Jones by calling the bad/low-percentage plays only when Jones is in the game, and then immediately figures it out once Zappe steps in and calls the "good" plays.
It seems much more likely that the play-calling is being made with the input of, and at the behest of the QB. Jones probably prefers less pre-snap motion, doesn't like turning his back on the defense with play-action, likes the downfield concepts that mirror what he did at Alabama. Zappe, on the other hand, ran an air raid offense in college and naturally will be more comfortable with shallow-crossers, stick concepts, so forth. And it's not like Zappe hasn't thrown the ball downfield - he has, and he's done it pretty good job at it.