I can think of a really strange idea about secessions. You know how control actually refers to realm control? Well, so long as the control is Main or above, that technically means the realm has a fairly strong leash on the region. I'd say don't let a duke secede while control over his city is at Main or above. Add to that the ability for taxes on the city.
So how to balance these? Let those council-imposed taxes decrease realm control slightly for every day they are in effect, with the control lowering effects scaling with the tax rate imposed. This means evil tyrants can't keep dukes imprisoned within their own city unless they seriously dedicate a lot of police and the judge keeps holding harsh courts there. Even then it's not guaranteed to keep the region at above Main. On the flipside, this would mean that the duke needs to consider more the trade-off. Is it really that bad in the realm that they should sacrifice some stability in order to sever with the parent realm? Are they really that intent on being their own realm as opposed to keeping their current position?
I'd say that the stats penalty after secession would still apply, such that a recently seceded city would be at around Occupied control immediately after secession, meaning you better hold courts and do police work. It shouldn't be that easy to pull off. You should have a good plan post-secession. As of now, for some duchies, it's all too easy just to click the link and let your new realm sort it out on its own with estate coverage.
My only thought here is that the realm control in the mind of the minor nobility and peasants is represented in the person of the Duke/Duchess. They owe their loyality to the realm via their liege and not a direct oath to the realm itself.
