Being morally grey is one thing. Doing horrible things and getting away with it is another. Discord did a horrible thing in s9, didn't apologize and got away with it. And really, you can argue that the trio were just imprisoning him after graciously letting him go. What makes his actions even worse is that this was the third time he did something horrible after being given a second chance after said second chance took place after he expressed no remorse. After a while, you got to question just how much one could get away with as long as they say their sorry when others don't even get nearly as much chances as them.
Yes, everyone should have argued against turning them to stone, but we got to remember that it was Discord's idea after he led them along. He did it with a grin and begged Celestia and Luna to let him/join him. As for the murder attempts, they were literally in a fight. And really, the trio seemed to be oddly merciful in not killing anyone, even when there were plenty of opportunities to do so. As for the promise of coming back, I see that as no different to when Discord mocked the ponies for trying to reform him right after they were gracious enough to let him go.
The fact that the princesses decided to punish them in such a manner and no one stepped in to protest after all the villain reformations they saw is hypocritical.