I would not surprised if she would be in a secret aliance with Mehrunes Dagon. She would still win even with the destruction of Morrowind. The dumner will look upon old goods who they have forsaken.
Of course she was. The events of Morrowind are completely her own machinations (with a little bit of Uriel Septim's thrown in) and what happened? The Heart of Lorkhan, the stone of Red Tower, left Red Tower unpowered, leaving only one more tower left in order for the barriers to collapse against Oblivion's Red Tide. She actively worked to end the 3rd Empire.
http://www.imperial-library.info/content/nu-mantia-intercept
But look else at what it did, she reformed the soul of the Dunmer people so that it would be slightly more amenable to those taking them in. They got rid of their slaves, began to overcome their xenophobia/became more amenable to Imperial (read: universal) values, among other things. What does this prelude towards? Them becoming a people of refugees, abandoned by the philosophy they adhered to when the mortal center of it died. For what purpose? Who knows yet. That is manipulating events not just in your favor (vengeance against the Tribunal), but also showing kindness and consideration for one of Azura's patron peoples.
As I said before, she is what she is, the Daedric Prince of Transition. Her actions always end one thing to begin another. You can ascribe one reason for that transition (it's petty, it's wrathful, it's kind, it's merciful, it's manipulative), but you'd be doing both Azura and the people undergoing that transition a disservice.
Considering what happened with Numidium at the end of Daggerfall (or what Tiber Septim was able to accomplish with it in his day), which was "only" using The Underking's soul for power, I don't think Akulakhan being activated with the Heart of Lorkhan would've bode well for anyone.
Yeah, were I Dagoth Ur, first act I'd do with a fully powered Akulahkhan is give the world Corprus. Or at least the Dunmer peoples.