In Norse mythology, as well the mythology of various mythologies throughout history, the trickster in their actions often in the end bring about change for the betterment of humanity. Witness for example, the formation of the 616 Avengers. Had it not been for the plotting of Loki, Earth's Mightest Heros would probably not have been formed.
In the Ultimate Universe it is quite reasonable to infer that in the end this ordeal would bring the Ultimate team closer together and give them more cohesion. Furthermore, with the uncertainty of Thor's "God" status Loki could be using this opportunity to prove that Asgard and the gods associated with them are a real.
Tricksters although they are mischievious aren't evil to the degree that they can be seen as incarnations of the "Devil'. I know some people will argue that in the case of the Ultimates that the wholesale death and destruction in this current arc merits comparison to the Devil. In the end the actions of the trickster in many cases makes mankind pay greater attention to what is right and good.
OR MAYBE ALL THIS TALK ABOUT GOOD AND EVIL IS RELATIVE DEPENDING ON PERSPECTIVE AND CULTURAL AND RELIGIOUS BIAS OF COURSE