I just read the end of Stormwatch a few weeks ago, and it felt, to me (as much as I loath psychoanalytic readings of writers' motivations) like Ellis was just plain annoyed at all the the red tape and politicing that he had to write into Stormwatch, so he built a team that would simply ignore such things.
In a way, Authority is like his personal power fantasy, all the things he'd love to go around world doing, given infinite power and resources. The soul of the book seems to be "fuck it, let's just do what we think is right." I feel, though I have not yet been able to locate in the text, that this is meant as dark satire, that Authority is supposed to be the logical progression of what a superhero team who thinks they know what's best for everyone would actually do. Given the freedom and power to act as they please, Jenny goes from not caring about anything to being a crusader for... something, and Jack and Swift go from nigh pacifists to enjoying killing people.
A lot of readers didn't take the series as dark satire, of course, and the writing itself wavers back and forth a lot. Seems to me that the Millar run was either so deep into the satire, from the characters' points of view, that it lost the little wink at the reader that indicates satire, and/or Millar was just getting off on the killing and the violence.
But that's beside the point, really, since the bulk of readers seemed to be doing the latter, and the readers' responses that have far more influence than the artists' intentions.