Yes I was talking about the Templars, and no they weren't going to kill or harm Rhys, they weren't an immediate threat to him at all. They were doing their job. Standing guard. Their deaths weren't necessary in the slightest, who gained from their deaths? Cole was invisible, and could just have easily knocked them out, instead he slit their throats and let them choke on their own blood.
Before someone brings up the fact that Leliana also approved of their deaths, she was in the wrong too.
Look at it this way-
In DAO, you needed to get Anora out of Howe's estate. In order to get her out, you had to kill Howe's guards. Some of them were probably innocent. But you killed them all the same, because they had to die so that you could help Anora.
In Asunder, Cole needed to get Rhys out of his cell. In order to get him out, he has to kill the Templar guards. Some of them were probably innocent. But he killed them all the same, because they had to die so that he could help Rhys.
And I'm not no sure about his options here. He was new to using his powers at will, and he struggled to remain hidden long enough to slit their throats. Now imagine if he'd had to knock out 2/3 heavily armed and armoured Templars, hope they stayed unconscious long enough to get Rhys out of his cell, and hope that they wouldn't join the hunt for him after they'd come round.
Edit: At any rate, my point is he killed to protect Rhys. And it was his decision to do so. So I think he's capable of making a choice about who he does or doesn't want to fight/kill when in the Inquisition.