The Orions were killed for what they knew, the same reason T'Prynn was given to terminate Quinn. Nogura followed his orders, T'Prynn did not.
If T'Prynn had been told to exterminate the Orions...do you think she would have disobeyed the order?
It was more than just about "what they knew". It was what kind of people there were and what kind of threat they might be with said information.
No, they were not the same.
And comparing the situation with the UFP and the Shedai with the Shedai and the Tholians...again, context matters.
Were the Tholians seeking to exterminate the Shedai? Were they even capable of it?
That WAS the case with the Shedai, and Starfleet was not even knowingly torturing them. Imprisoning them, yes. And I'm totally cool with that, considering what free roaming Shedai usually meant.