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 there's one exception then there are usually others. What Nogura ordered done with the Shedai was pretty much the same thing that the Shedai did with the captured Tholians. Does that mean that the Shedai were right to do what they did or is that reserved just for humans?
Starfleet, through Nogura, pushed for the project to proceed faster than it should have in the name of power. Years lated David Marcus even said that the Shedai tech could be perverted into a dreadful weapon. McCoy even saw that as the first consequence of Genesis. No wonder the Klingons were so eager to possess it's secrets. Their neighbors had just developed the planetary level neutron bomb and claimed that it was only for peaceful purposes. "Trust us, we're the Federation".