You're correct in that the Heartwights do in fact have more power. Like Dagoth Ur, they are directly "plugged in" to the Heart. That is why, according to lore, even if you kill them they do not die. They sooner or later resurrect near the Heart and then return to their citadels. The other followers; from Ash Slave to Ascended Sleeper, do not have that direct connection, so when they are killed, they die permanently.
The creator of the GHD mod and I have had a lot of discussions about Great House Dagoth as well as the mindset/personality of Voryn Dagoth and we are both in agreement that not even Dagoth Ur, a mortal turned demi-god, could micro-manage everything, so a level of personal independence in his followers would be looked on favorably.
Again I refer to the dialog, and I am not referring to dialog added by mods that let you join House Dagoth. The higher ranking members have "normal" dialog. Yes, some may argue that the fact that they support Dagoth Ur is insane in itself, but again, I am referring to the fact that they are not just standing around muttering to themselves about how the furniture won't keep quite. The high ranking ones who earned the "Dagoth" title are speaking normally and doing their own thing. And these people who are showing independent thinking are placed in charge of their own bases.
And as far as why Dagoth Ur chose the methods that he did to fight against the Tribunal; here is one of Voryn's responses from the game:
"If, by my crimes, you mean the inevitable suffering and destruction caused by war, then I accept the burden of leadership. The Sixth House cannot be restored without war. Enlightenment cannot grow without the risk of upsetting the tradition-bound and complacent herd. And the mongrel armies of the Empire cannot be expelled from Morrowind without bloodshed. As I have charity and compassion, I grieve. But our mission is just and noble."
That doesn't sound like one who relishes death and destruction. He doesn't like it. But there is a war going on. War brings death. And as far as why he started the war in the first place and used the blight as a weapon; I attempted to have Voryn explain that himself in my fic when he says to my player-character;
"I alone did as Nerevar asked and for that I was struck down and have been mocked by the Tribunal. Before you judge me any further I ask you, Aeronwen, what would you have me do? Should I allow the Tribunal free access to the Heart so that they can recharge their 'divine' powers and continue to lie to their followers? Shall I just sit quietly in my citadel and allow them to do as they wish? Perhaps I should put out a red carpet and serve drinks. Is that it?"
Most of his House had been killed off by the Tribunal, he was beneath a mountain, behind the Ghostfence and with limited resources. He wanted vengeance against the Tribunal and to take back the land that had been handed over to the Emperor so he used what was available to him.
I am NOT saying that he is entirely sane or that there is nothing wrong with the methods he used, but I don't think he was a deranged tyrant who wanted to rule over a land of mindless, tentacled puppets. That may have been the result in many cases of people being exposed to the Heart, but I don't believe that was the objective Dagoth Ur was aiming for.