NERD FIGHTThey freed the sentient species when they realised it was sentient, didn't they?
Keeping wild animals in captivity isn't allowed by the Federation, presumably in case one of them ever turns out to be sentient. Good call by whoever wrote that rule down.
Plus, they didn't actually release it
because it was sentient, they only released it because it was going to die anyway - they were using it as a slave even
after they knew it was sentient.
And the genetic experiments, I present exhibit Julian Bashir.
Despite happening over a century after Discovery, Bashir's father was literally sent to jail for engaging in genetic manipulation. Julian, despite not being culpable for the process inflicted upon him and an outstanding service record, still barely kept his job, and people openly distrusted him after it came out.
I present counter-evidence: that stupid episode about Riker working on an (illegal) invisible starship that one time. They used it as a bookend for the final Enterprise episode that everybody pretends never happened, but it established that the Federation has strict controls on what kind kind of technology programmes it can pursue even in wartime.
I forget which Federation citizens they kidnapped and executed...
The crew and passengers on the prison shuttle in the first/second episode. The lead character of the show has essentially been press ganged.
and the covert weapons programmes, well. Beyond the Spore Drive I forget about that too,
The ship is a covert weapon full of covert weapons development programmes. This is the actual setup of the show.
other than the blowing up the Klingon homeworld thing which I thought was an idea from Mirror Lady.
It doesn't matter who came up with the idea, it matters who actually carried it out - mainly the lead character's dad and that admiral, neither of whom are punished for it despite going to lengths to hide what they were up to
specifically because they knew it was illegal and their subordinates might not go through with it.
They're good people
Being less bad than others does not make them "good". These people are criminals and at the very least they should be split up and assigned somewhere else. The lead character's crime wasn't "we just didn't know her that well at the time", it was mutiny and assaulting an officer (plus she was - rightly or wrongly - personally blamed for starting the war), and her best case scenario at the end of STD was being released for time served, not elevation to one of the highest positions in the fleet just because she (checks notes) followed the rule of law.