It seems most people on here seem to say it's fact that the original Nerevar was killed by his loyal friends, the Tribunal and then they went on to become gods. But then I also see other accounts in lore that say he was wounded beneath red mountain, and died of wounds from his battle with Dumac.

In Morrowind when you question Vivec personally if they murdered Nerevar, he says personally that they didn't kill him and that story is false.
Vivec will then direct you to two sources pulled out of the Tribunal Hierographa and Apographa, which you can go take your own copy of.

One source, is from the verbal accounts of the Alandro Sul, shield companion of Nerevar, titled "http://www.uesp.net/wiki/Morrowind:Nerevar_at_Red_Mountain". This story is always varied because it was never recorded on paper by ashlanders, but the same story was almost the same. Nerevar was murdered by his kin through trickery.

It says at the battle of Red Mountain, when the Dwemer race disappeared from the face of nirn and Nerevar recovered the tools of kagrenac, he gave them to dagoth ur to guard while he went to talk to the tribunal for advice on what to do with the tools.
Nerevar then asked them to help him summon Azura through a ritual to get guidance from her. But the Tribunal, already corrupt by the tools (though having never even seen them yet) pretended to do a ritual to summon azura, but actually poisoned Nerevar through the fake ritual and killed him. Nerevar was murdered by the Tribunal.
Then in that instant Azura showed up and cursed the chimer turning them all dark skinned, the entire race included. They laughed in Azura's face and told her that they would use the tools to become gods (again this is before they have even made contact with said tools). They then all went to red mountain, and fought Dagoth Ur for the tools, and he fled in the battle. Then they turned themselves into gods and the rest is history. *Do note however, that his account has absence of Nerevar's 'betrayal' of Dagoth Ur, which he says personally happened at the end of the main quest in Morrowind. It is clearly stated that Nerevar left Ur to guard the tools, then came back and got into a battle over the tools, thus the betrayal in the eyes of Dagoth Ur, but this source says Nerevar never made it back to Red Mountain, questioning the validity of this source.

The Second source, is the words of Vivec when questioned by a Dissident priest Malur Omayn, during the time of the Main quest in the game Morrowind about the Nerevarine prophecies and the outlander claiming to be the Nerevarine, titled "http://www.uesp.net/wiki/Morrowind:The_Battle_of_Red_Mountain". (you can actually hear about this guy getting questioned in the ministry of truth partway through the main quest, by asking about Latest rumours in Vivec city.) So this is like within weeks of when the Nerevarine meeting Vivec personally.
This is all written in the first person if Vivec himself, talking about the same account as the first source by Alandro Sul.

What it says basically is that in the battle of Red Mountain, Nerevar and Dumac struck eachother down, mortally wounding eachother. In that instant, Kagrenac saw that their king was losing, and used the tools on Lorkhan's heart and what followed was the disappearance of the Dwemer utterly and completely. Nerevar and Dagoth Ur found the tools, and Dagoth Ur said that the Dwemer destroyed their race through use of these tools, and they should be destroyed lest they fall in the wrong hands. Instead of destroying them then, Nerevar wanted to go talk to the tribunal and get their advice, as they had told him in the past to go to war against the Dwemer and he refused to listen because he was good friends with Dumac. (until they found out about their heretical use of the Heart to try and make their own god)
He was then apparently carried from Red mountain, as his wounds were still bad and met with the tribunal, telling them all that happened. The Tribunals advice was to preserve these tools, incase the Dwemer didn't kill themselves but just went to another realm, and might come back for another war. Nerevar accepted this under one condition, they make an oath to Azura that they would never try to use the tools in a profane manner as the Dwemer had. They all then accepted and swore oaths to Azura and Nerevar.
After that, they went back to Red Mountain and found Dagoth Ur guarding the tools. They said they were going to take the tools and secure them, but Dagoth Ur was acting erratic, saying only he could be trusted with the tools. Vivec says here that he acts delusional, maybe gone mad from the tools but later believes Dagoth Ur at this point found out some secret in the use of Kagrenac's tools and wanted to covet them himself. It inevitably led to conflict, and Nerevar fought his loyal servant Dagoth Ur. In the battle, Dagoth Ur and his retainers managed to escape.
For some amount of years after (it doesn't say how many years), they kept their oath to Azura and Nerevar. Sotha Sil studied the tools in secret and eventually came to the rest of the Tribunal, telling them how they could use the tools to become gods of their own, that actually cared about their followers, as they live in the world as mortals and know what it is like. With the vision of a better world, they went back to red mountain and used the tools to create themselves as gods.
No sooner when they discovered their new powers, Azura showed up and told them that her champion Nerevar, true to his oath will come back and punish the Tribunal and also make sure no one ever uses the heart for such a thing again.
Sotha Sil then basically told her that the daedra are distant gods who care nothing for man or mer except as playthings and they will be gods that care about their followers.
In that instant the chimer were changed to dark elves and azura told them it wasn't her doing but their doing, for mocking the gods. The tribunal then went on to become gods and the rest is history. *Do note this one source has the absence of the death of Nerevar. They sort of make it unclear where he died, whether it was at red mountain during the fight with dagoth ur or later.

So quite a bit differs in the two accounts here. In vivec's own words he says they didn't murder nevevar, but was he lying? The fact that dagoth ur says Nerevar betrayed him beneath Red mountain seems to make the whole account by alandro sul to be false. In that source, Nerevar never even makes it back to Red mountain in the confrontation with dagoth ur, but we all know he says at the end of Morrowind that he was bitter about Nerevar's betrayal.

So my final question is, How did Nerevar actually die? It seems theres more evidence that he was wounded beneath red mountain and died later, then getting murdered by the tribunal.

Edit: added in links to sources.

http://www.imperial-library.info/content/foul-murder