According to the portion of the Prophecy for D3, the comet bears an omen, a foreshadowing of things to come, not that the contents of the comet is itself evil. It very well may be Tyrael. I have no doubt he shall go true Rogue in D3, but what he does he does for the good of Sanctuary. He gathers together the strongest of warriors in the hopes of uniting them against the Heavens, as the Heavens have witnessed the innate power of mankind and fears that, should Hell consume all of Mankind, the Hellish powers unleashed would be unstoppable.
Think of it this way, in StarCraft terms. Tyrael is Tassadar. Tassadar was charged with humanity's destruction for the Protoss feared the power the Zerg would have should they gain psionic potential. However, Tassadar turned his back on his people and attempted to save mankind while simultaneously fighting off the Zerg. Ultimately, however, his actions would bring destruction upon him and his loyal followers.
Tyrael fled heaven and warns mankind; in righteous anger, Heaven's luminaries, failing their age-old task of protecting humanity, come to destroy it so that no other power [ie Hell] may possess their innate powers.
Hell is caught up in another Civil War, leaderless without the Prime Evils. Diablo, Mephisto and Baal likely don't care whether they live or die, so long as their respective legacies live on and ultimately achieve their goal: the downfall of all creation through terror, hatred and destruction. Diablo inspired terror in the hearts of the masses; Mephisto's hatred took root in the minds of the leaders of the lands; and Baal sundered Heaven's solidarity (in that Tyrael overstepped his bounds, and now there will invariably be followers of Heaven and followers of Tyrael).
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Be it through hallowed grounds or lands of sorrow
All in the Forger's wake is left bereft and fallow
Is the residuum worth the cost of destruction and maiming;
Or is the shaping a culling and exercise in taming?
The road's goal is the dark Origin of Being
But be wary through what thickets it winds.
-Excerpt from the Litany of Residuum;
As Translated by He Who Brings Order