This is not about something IC, its about not being able to destroy a realm.
That is a circular argument. 'You can't destroy the realm because destroying the realm would destroy the realm.'
It's pretty simple: this is an area where BM-the-game is getting in the way of the players doing what they want to do because, as you say, they might screw it up and do something with poor results that can't be un-done. Okay, that's at least a valid concern. What are we accomplishing instead?
Zombie realms with joke governments that have to have non-wars with friendly neighbors so their regions can be 'taken over.' Nobles fighting other nobles on the battlefield, usually by accident, because you can't 'take over' without a declaration of war.
This is the game mechanism equivalent of life support for a terminal patient. I understand that you don't want a legit one-Duchy realm to have a 'end realm forever' button, but it seems like this could be circumvented easily enough with a minimal amount of design: for instance, allow any region to 'change allegiance' to a realm that no longer exists but did exist within the last month. That solves your problem and doesn't cause mine and you eliminate the potential damage a crazy Duke can do if the rest of the realm isn't on board.
If its already proclaimed dead, become ruler and make the capital a separate duchy
It says you can't secede the last city, not the last Duchy. I can save some time by making a new Duchy out of the neighboring townsland and having that secede, but that is really, really gamey. Congratulations, you're a Duke! No, not really, just to do this paperwork.