I wasn't arguing the morality of their actions, just that they had official sanction hence wouldn't be necessarily punished for their actions.
But why is that the overriding factor in determining how we as an audience
feel about their actions? That's what confuses me, that people seem to be getting angry about what they did for reasons that are strictly about legal and bureaucratic technicalities rather than identification with characters' emotions and intentions...
You are making exactly the point that is bothersome.
When the team is sent on an explicit mission and they have to kill someone, they are not acting for themselves, they are acting for the agency, and we presume there is some greater good. (This may be challenged by The Winter Soldier, which will be a fascinating story.)
In acting to save Skye, they are acting only for their own motives, and so what we saw on screen during that hour was the sum total of their motives, objectives, and methods.
In this way, they are subject to audience judgement in a way that doesn't happen when they acting for the agency. This was an explicit part of the story.
The writers could have created a story where a scientist or witness who had valuable, irreplaceable information had to be saved at all costs. This would have taken much of the morally grey area out of the story.
The writers didn't choose that type of story. They chose a story where the team was acting out of their own emotional attachment to Skye, and without any sanction from any authority. The legal, moral, and emotional issues are completely visible within the episode and are put there so that the audience can experience them.
The story was written so that, hopefully, the audience would think about these issues.
The issues aren't "stupid" as some posters here have implied, and neither are they black and white. They were given to us purposely by the writers so that we could have this discussion. Or, possibly, the writers didn't think things through, or didn't think anyone would notice.
There have been some interesting theories that Skye may be Jessica Drew. There is nothing conclusive there, but if Coulson et al were being influenced by pheromones coming from Skye, this could easily explain them acting rashly. As well, the GH25 may react differently with her metabolism than it did with Coulson.
The episode is interesting if there are consequences to explore. What I don't understand is the argument from so many that there should be no consequences, and that the actions of the team weren't even borderline.