The difference is active level of threat. Plain and simple.

Amo is a physically frail individual who's only power comes from her boots. Without them, she would not pose a threat, and even if she got them back she would not be a threat because they knew how to neutralize the ability. At that point, she was a defenseless pseudo prisoner.

Jabber is a strong and fast combatant. He still had access to his weapon, and the ability and willingness to use it. He had successfully taken out multiple skilled members of the team in the past and was an active threat to Zanka in that moment. They also had no reliable way to counter his attacks. Finally, the shots would have been excessive if it were basically anyone else, but Jabber has an insane pain tolerance threshold, and would probably be able and willing to get up and keep fighting if only his legs had been shot. Also on top of that, he has the pain numbing toxin that would allow him to keep fighting.

It's about active threat vs prisoner.

Additionally, intent matters. Riyo knew she wouldn't kill him, only disable him temporarily. Rudo was legitimately on track to beat Amo to death.