Did the emperor actually know that Akulakhan was being built?
By the way here`s the part of the decoded letter that suggests the emperor thought that the Nerevarine would drive away his people:
"His Majesty's particular wishes are as follows.
A local superstition holds that an orphan and outcast, a youth born on a certain day to uncertain parents, shall unite all the tribes of the Dunmer, drive out the invaders of Morrowind, and shall reestablish the ancient laws and customs of the Dark Elven nations.
/.../
%PCName has the appearance of meeting the conditions of this local superstition. Therefore it is his Majesty's desire that %PCName shall, insofar as is possible, satisfy the conditions of this ancient prophecy, and shall become the Nerevarine."
Well, even this could be interpreted in many different ways. The Dark Elves were invaders of Morrowind long before Imperials had even thrown off the yoke of the Aylieds, and you also have to look at the timing of the prophecy, which Uriel Septim and his ministers would have done.
The prophecy surfaced as the tribes were pushed further and further from the airable lands of southern Vvardenfall. To them, the lords of the three houses would be considered invaders, or possibly, "Invaders" meant the warped monsters of Dagoth Ur reborn, because they would often attack villages, and were very dangerous, provoking Uriel's response.
Still, invaders may have meant outlanders, but if that is the case, then I believe that Uriel would have counted on a Morrowind with a weaker Tribunal after the Nerevarine Prophecy, thus, far easier to reconquer if they rebelled.
PS, after a little research, I found no primary document saying that the Nerevarine would even kick out the outlanders, this only appears in imperial works on the prophecy.