For quite some time, I've wondered whether or not the denizens of the Pegasus Galaxy found Team Atlantis to be a beneficial addition to the population, considering all that has happened since the SGC sent the mission to the Lost City in the first place. And I've always thought that it would have been a more interesting show if those in command of Atlantis (particularly Weir) had been forced to defend their decisions to others. For example, during roughly the same time in the Stargate continuity, SG-1 was defending themselves against the IOA.
I think the idea of the various human communities in the Pegasus Galaxy coming together in a coalition is a very good one, and one that should be maintained over the course of the rest of the series and the impending TV-movies. In a way, it legitimizes the idea of calling out Team Atlantis on their decisions. Previously, there was no one else out there willing and able to take the unilateral actions necessary to fight the Wraith, the Asurans, and Michael. Now that time has passed and the human societies have come together, they have the right to ask Atlantis to play along and consult them.
It also makes a lot of sense for them to question the decisions that have been made. They can't argue the fact that they woke up the Wraith, and they definitely can't argue the fact that they were directly responsible for creating Michael. They bear responsibility for those actions and dozens of others. The fact that they've saved millions after the fact doesn't absolve them of the need to atone for those mistakes.
So I was a little annoyed when the writers chose to have the coalition go so far as to put Team Atlantis on trial without due process and in the most questionable manner possible. Not only that, but ultimately two of the judges were corrupt. One had already decided that Team Atlantis was guilty, based on an irrational desire for revenge, and the other had been bribed by the Genii.
The net effect is to render the points brought against Team Atlantis completely invalid, because they are framed as biased. This is despite the fact that Sheppard and Woolsey were unable to give strong and compelling arguments in defense of the expedition! Woolsey essentially has to match the Genii in terms of persuading one judge to vote in his favor. The bottom line is that the very real issues brought up by the coalition were never really addressed.
This leaves Team Atlantis with a false sense of righteousness in their decisions and actions. It's unlikely that they will change their thought process in any way as a result of the "inquisition", and that means that the coalition will probably be seen as more of a nuisance and impediment than an example of a rising good for the Pegasus Galaxy. It's pretty much typical of the Western view: indigenous populations don't know what's best for them, and they cannot function without the "enlightened" actions of those more knowledgeable.
It might have been better if the coalition had been treated more like the Jaffa on "SG-1". Generally speaking, the SGC stood for the rights of the free peoples of the galaxy against the System Lords because the free Jaffa weren't ready to step up to the plate. Once they were, it was more of a partnership. This episode firmly places the moral superiority in the laps of the Atlantis expedition, and I think it would have been a lot more interesting if they were left with a little more doubt in the rightness of their actions.