Board Thread:Anime/@comment-27321453-20180722183806/@comment-1327106-20180725203941

I don't remember them rescinding the order at the end of S1, but I could be wrong. I do remember Erwin justifying his actions and promising to root out the other Titans hiding among them, but I don't think we hear anything from the government's side of things.

Eren was supposed to be handed over to the Military Police after Trost, which is why they had the trial, but I believe Zackly was the one who make the call for who should have custody of Eren, as he's head of the military (but not part of the inner government). As to why they had the trial at all, I assume it's because the SC protested and Zackly decided they would do all this nice and proper through the usual military channels and he had no reason to override Erwin's request.

It's possible that the government also did not think Zackly would make that decision, and once he did they could not easily undo it without drawing attention to the fact they were overriding him. (Zackly would likely want to know why.) The failed expedition would have been a good excuse to change things.