I get why they want to show the "The federation isn't flawless either" argument, but it is being done in the most hanfisted way possible.
The most recent episode of Strange New Worlds was an okay take on it, highlighting some hypocrisy in it all, but we really don't have enough information on the legal system to understand if any of it even matters.
I agree. The Federation as a well established monolithic structure around exploration, peace and dialogue helps frame everything else that happens in the show.
Throw that out of the window and what are we left with.
Maybe it is just a symptom of this whole "This is THE HERO" thing that popular story telling has shifted towards. Picard was undoubtedly an important and great captain. He certainty had those "everything hinges on what he and his crew do next" moments, but there were always others out there alongside him. Losing Picard was a blow to the federation when he became locutus. But it didn't break them.
Now watching more modern Star Trek it feels like the only people worthwhile in the entire federation are the people on screen right now and their renegade shenanigans.