Bear in mind that this doesn't preclude rebellion of some sort. Mannfred rebels all the time, often loudly and with explosions. Arkhan rebels as well, albeit in more subtle ways. So does Neferata.
Think of it like Doombots. Dr. Doom (bad guy from the Fantastic Four, if you're not familiar with comics) makes robot doubles of himself to undertake dangerous tasks, enact certain schemes or to do the stuff he doesn't want to bother with. These doubles are so perfect that they assume that they're the real Doom, unless he's in the room with them - and even then, some of them maintain a strong suspicion that they're real and he's not. And since they think like Doom, they act like Doom. So they plot and scheme against each other (and the the real Doom) because there can only be one Doom, and obviously it's them.
Basically, Nagash has absolute control, except when he doesn't, because his servants are all to one degree or another shadows of him. Which means that like him, some want to be on top and they'll knock over anyone they have to, to do it. Including him. If he's paying attention, he can swat them down without any real difficulty. But if he's not (say, because he's preoccupied waging war on Sigmar, Archaon et al), then there's a good chance they might get away with it for a while.
So if you want your Death leader to be a rebel against Nagash, the established meta-narrative is flexible enough to fully support that. Same as if you want them to be an unwilling slave of Nagash, a contented servant, or an unwitting dupe.
At least in my opinion. Your mileage, as they say, may vary.