Some drumhead court-martial, lifelong prison sentence, violently separating a mother from her child and some goons beating up a prisoner

The key point here is that it is portrayed as horrible. Ake resigned in protest and only came back for the opportunity to make amends. The scene is there to show how far the Federation has fallen, in order to set up the task of rebuilding it.

Starfleet Academy has a justification for how shitty the world is, and IMHO it’s approaching it correctly. There was a galactic disaster that almost completely destroyed the federation, so SFA is literally post-apocalyptic. But it’s using that setting to tell a hopeful and positive story.

The core message of the show is that you can rebuild a just society even after it’s gone so far down the shitter. You can choose to do better, to be better. This is culturally relevant.