I think you are missing the whole point of the Nerevarine, fate, and the hero.
Usually history is written by historians who are either heavily subjective and know so, or trying to be apathetically objective and do so.
It is a 2 way deal, everyone needed the Nerevarine. The Nerevarine was the keystone in this saga, without him the entire crisis could never have been solved, the emperor's "plans" crumbled (I doubt he even knew what the heck was going on either) and fate could not have been deilvered. The Nerevarine was vital... But you dispense with this name as if he was some random drunk from a tavern, who just "hapenned" to save Tamriel. Uhuh, the Nerevarine by the fates was destined to be the Nerevarine. He could very well have been that random drunk, but he was still going to become the Nerevarine; get corprus, fullfill the prophecies of the Seven Visions and free the Heart, and the other drunk just died in a ditch somewhere. The Nerevarine was directed by powerful entities to his destiny, yes, but the "plans" of those people revolved around the Nerevarine, the Nerevarine did not revolve around the plans.
I'm also missing something in this discussion. You all seem to assume that the Nerevarine would take the throne if he could. But why should he want to do that? Why would the Nerevarine want to become king? Is becoming king the final purpose of the Nerevarine or was he only needed to end the rule of the Tribunal and begin a new age for Morrowind (by helping Helseth).
I don't agree with all that TSBassilisk said there. I do not think that the empire had it's disposal the power to completly eradicate Morrowind. If Tiber Septim has such great power, then why did he agree to an armistice? No, Septim did not have power enough to crush Morrowind and Three Living Gods and then still carry on his conquest of Tamriel. Morrowind would have crippled him and itself be destroyed in the process.
Either way, I started off asking why Nerevarine didn't take the throne, seeming that Nerevar the figure was a king. However, now since we know that could never have happened we're asking why didn't the Nerevarine kill Helseth, due to the apparent transgression made by the King on the Nerevarine.
The Dunmer will go back to the Daedra, I don't see them wanting to or being able to serve the Nine. It's a different mindset, an alien array of customs and would become simply another affront the history of the Dunmeri and their Chimeri ancestors. Saying that is like being a roman citizen and speculating that the Jews would all convert to the roman religion when the 2nd Temple was destroyed. They didn't convert, but now the roman empire is gone but judaism lives on.
Yes, the civil war was becuase of slavery. Same with america when it's slave trade was threatened, there was a civil war... My american history is as deep and an empty cup of tea, so I'll stop there. But that is not the point, and I'm not saying that Helseth is "evil", just that's he's a kniving bastard, a generic Hlaalu n'wah who says he wants the best for everyone, but secretly puts all his eggs in the House Hlaalu basket; leaving everyone else to starve.
No, Licoln was not evil at all, but the civil war was an evil thing and I think that slavery could have been abolished through social progression and reform. What's done is done, and we're talking Morrowind, not America.
Same with Helseth. I very much doubt that Helseth erupted civil war on the province of due to some "genuine concern for the beast races"... This coming from a man who uses the Dark Brotherhood to murder potential rivals, and even set them against his own mother. Hmm. Put him in a mushroom tower in the middle of the Boethian Mountains... There you go, a good Telvanni, not a good ruler of Morrowind I think.