Give all Duchy titles to one of your courtiers - without dependencies. When he (or his heirs) revolts some years later, you could let him become independent (you'll be able to reclaim his county later on which should make him landless, I think). Haven't really tried this yet though, as this is quite 'gamey'...
Well, I'm one of those weird players who never edits or reloads, but happily takes advantage of every gamey exploit I can identify. So, I have tried this.
Unfortunately, it's a bit more difficult. Probably difficult enough that you might revise the "gamey" appellation. When you give the duchy titles away, the recipient becomes liege of those counts. So, when he becomes independent, he takes those counts with him. Not to mention that granting him independence lowers your crown authority.
So, what I've started doing is, after a duke rebels, and I seize his duchy, I keep it for awhile and try to encourage his former counts to rebel (and the newly demoted count to re-rebel). Don't resolve those wars until you've got all that duchy's counts in revolt and occupied; obviously this could take awhile. Only when you're able to pull most/all the counties do you pause, give away the duchy, BEFORE spinning off the counts to new vassals.
The target recipient of the discard duchy should be a terrible one county vassal, with as many negative traits as you can find (you're hoping to foster revolt between any future counts and him). Ideally he'll be near muslims or pagans, as well. Hopefully giving him the duchy doesn't give him suzerainty over too many counties, but you're not always going to be able to time the revolts and hand-overs perfectly.
Once you've got your duchy dumpster set up, don't rush things, he'll be a terrible vassal, but you may be able to throw multiple duchy titles his way before he revolts. He'll get more and more negatives, but if he only controls one county, he's generally not too eager to push things, too quickly. Besides you still get the prestige for having those duke vassals until he actually revolts.
After he revolts and you surrender, start trying to generate a claim on his county(s) (more convenient if you already have one, though I'm not sure if you'd lose it in the surrender). After the truce, you declare war and take his county, poof, duchies disappear. If you're fortunate, some muslims or pagans might do the job for you, but how lucky do you feel?
Bit difficult, lots of micro-management, and timing is tricky, so it's probably not worth it, but if you're a perfectionist, it's the only way I can figure out within the game system to minimize the number of duchies, if they're already been created and you're already suzerain (i.e., invasion aside). Waste of time for two county duchies, and probably not worth it for three county duchies, either. But if you can get rid of the big duchy titles, and you hold two yourself, you can keep the larger counties in your personal demense and still keep a lot more vassals happy.
Of course, invasions are tailor made for killing duchies.
