I've just got a few problems here, but you make a fair enough point.
The Great Houses have not been in civil war since the ascendancy of the Temple. The Temple, as we know stopped full civil war in Morrowind and brought the illusion of peace, but peace nonetheless under the Triunes. (Not only the Tribunal forbade civil war, but the Daedra too) All the conflict between the Houses has been trivial land grabs, petty slanderous squabblings and sabre rattling. The Dunmer, since the Chimeri days have always been a people of the knife, the heavily regulated and sanctioned Morag Tong assassinations are the tools to sate this subtle impulse.
Helseth comes to power and Morrowind really is plunged into civil war. Full civil war as Helseth engages a revolution against the people of Morrowind, backed by weakened imperial politics focused on the hope that the Dunmer will keep themselves busy whilst the imperials get their lazy asses back on their thrones.
The civil war was because he abolished slavery. I suppose that would make Abraham Lincoln evil for freeing slaves too. Of course, he didn't supposedly kill to get his position, but that's beside the point. And the Imperials are no more lazy than the Dunmer.
Helseth clearly has no inkling of how dire the crisis of Dagoth Ur was. If he did, he would have known that helping Almalexia, not opposing her every move, would have been better for the people of Morrowind in the long term. As we're talking about Helseth as a bad apple for the people of Morrowind, not whether or not he's entitled to do so or whether he's simply a good chess player, which obviously, he is.
Almalexia was out to get him. The temple was hostile towards him, because he refused to be a puppet. I doubt that anyone at the High Temple was even doing anything to stop Dagoth Ur. Almalexia sure wasn't.
Also, he tried to kill the saviour of Morrowind. This stinks of pure machiavellian knivery, most akin to Telvanni dealings. Why? Just the same reason why the mad god Almalexia tried to kill him, to maintain the order of power, and that means imperial sponsored Hlaalu cliency.
I believe that his reasons for trying to kill the Nerevarine were due to the widespread belief that he would drive out the outsiders and take over Morrowind; he was seen as a prophesied usurper. You have to admit, very little of the Nerevarine hype was about actually stopping Dagoth Ur.
Hypotheticaly, if he did succeed in killing the Nerevarine a few months earlier, he would probably would have doomed all of Tamriel.
That said, he didn't even have faith in his own culture's tradition enough to use the Morag Tong! He used the Dark Brotherhood, and y'know, those guys are just plain evil. Not to mention his vicious army of goblins, do you know how annoying those things were to kill?
Yet in Oblivion, he hires a Morag Tong assassin to kill the captain of the Drothmeri army that is planning on overthrowing the Empire. And Morrowind as well.
He's an imperial, ears clipped like a man swit and reliant on nothing but the weakening foundations that raised him. Yes, Morrowind needs and strong and pragmatic ruler, but a Dunmeri ruler, one who is intimate with the dunmer nation and knows the hidden needs of the nation. What isn't needed is an imperial imposter who think he can impress the Dunmer with shows of malice and radicalism.
Yet the Empire still stands. And what isn't needed is some ceremonial puppet king chosen to please the Dunmer by sitting around doing nothing. Besides, he's got Barenziah, who's quite intimate with the Dunmer nation [literally and figuratively]. And if abolishionism is radicalism, then there's no excuse for choosing anything else.
I don't support all that Helseth does. But I do point out that none of his alleged crimes have been proven.