I can already smell the hate boiling. Nobles are generally agreed to be the most worthless wastes of space since Soapmakers. They make horrible demands, order the hammering of dwarfs who could not have possibly completed their mandates, and generally bring a fortress to a spiraling death halt. This, in the nature of things, has lead to many, many people creating extraordinarily complicated ways to kill their nobles. And this, in the most un-dwarvenly tradition, in the most apologetic course of action, is my suggestion:
Punish them.
Not the nobles. Punish the players who kill the nobles.
Put down the hate chisels. Let me explain.
Dwarf Fortress is supposed to be a simulation of a fantasy world. It is, in fact, supposed to be a simulation of a fantasy world builder. How many fantasy stories do you know of where an important noble dies in strange circumstances and nobody notices or cares? You can probably count them on the fingers of one head. So, why not have a punishment system in place? It doesn't have to be super serious, like instant failure of the fortress. It should, however, require ingenuity and resources in order to avoid a worse punishment.
Here's the type of scenario I'm imagining:
The Duchess demands green glass items for the fiftieth time, despite the fact that this map still, consistently, has absolutely no sand. You, pissed off and tired of this ungrateful waste of flesh, decide to stage an "Unfortunate Accident." Namely, you have her pull a lever that drops her thirty z-stories into a pit. Some amount of time later, perhaps with the next Dwarf Caravan, the liaison comments on the missing duchess. Next season, you get no migrants. The next season after, a single dwarf comes with the title of Investigator. He begins snooping around the Duchess' chambers and, depending on how good of Liars your dwarfs are, eventually he investigates the pit and finds the Duchess' rotting body. He leaves hurriedly. Two seasons later, when you would be getting a caravan, you instead get an Inquisitorial Squad. They begin asking questions, and they aren't as polite as the investigator. They rough up your dwarfs a little, find out who killed the Duchess. (In this case, blame would fall on the mason and mechanic who built the floor, support, and trigger.) When they find the culprit, they take them into custody and either a) give them to the Sheriff/CotG/Hammerer, or b) take them away to the mountainhome, depending on what noble it was that died. In the case of the Queen or King dying, punishment should be much more severe, such as also taking your mayor, taking a percentage of your wealth, or even refusing to send caravans for a long time, up to five years. In more extreme cases, like repeat offenses, they may even lay a sanction on you, or even send an "honor guard" who take up the job of law enforcement.
Feel free to add thoughts on the subject. Please keep the hating and calling me an elf to a minimum.