An anti-item-scumming system already exists right now: The different item class preparations in the Bazaar. Even if you don't get the items you want to veto in your first run, you can easily bring out and veto items that "clogged" your shops this run to pretty-much guarantee that you'll find that specific item next run. Meta vetos.
Yeah, I know it's not elegant. But I guess we don't view going into a dungeon and, y'know, interacting with it in some way as an actual crime against life on earth.
Actually it is rather elegant, because it lets the ridiculously obsessive players have a large degree of control over a random system without removing the randomness that makes the game great.
It might help if there was more information on what items the bazaar preps get you. I for one am always perplexed by what 'quest items' means. A codex entry or item list would probably clarify what can be done with these preps.
Case in point: Waldo walking around stomping stuff. I'm pretty sure his big 'strategy' wasn't some kind of exploit but extremely high level gaming of the shops, veto slots and bazaar. I'm talking spreadsheets and probability tables to reduce scumming.
So it is possible to virtually eliminate scumming as long as you put the effort in, like many of the great old-school games with incredibly high skill ceilings.
If you grew up milk-fed on Call of Duty and Assassins Credd, it might seem strange to play a game that you are not able to 'clock' simply by putting enough time in.