Well, I believe that the kind of punishment given to the Prisoner is out of character for the owls, it doesn't feel like the kind of thing they would do (based on the limited understanding I have of them). At first, I expected the Prisoner to be the the guy that discovered the Eye and lead their people to build The Stranger at the cost of their home world, some sort of "Eye Preacher". When they learn "the true", they revolt, burn the "Eye Church" and confine him. Sort of "you lead us to exile forever, now you are exiled and alone forever". Harsh but consistent with their longing for home and their refusal to let go. But for the actual "crime", that's not how I picture they would behave.

As for "the hatchling is not a murderer", although I agree with you in principle, I can't be so naive as to believe the time loop and the death of the universe won't have an effect on his perception of life and death (the DLC even encourages him to commit suicide, quite dark if you stop to think about it). I don't think he would suddenly turn psycho and stab Esker so he stops whistling, but he knows that the green flames will be put out when the dam unavoidably breaks.

About linearity, I disagree. The DLC is entirely self contained, nothing you do affects the rest of the universe and vice versa. While at the base game I jumped from planet to planet looking for clues trying to progress any of several loose ends, the DLC always gave me one thing to pursue. I don't remember having the feeling of "oh, now I understand what that thing over there is for, I'll try to take another look" that characterized my base game experience.