The question is: if we had a chevalier companion, which of the known warriors would you ditch?
Oooh that's a tough one... At this point, it would have to be Blackwall just because we know very little about him and we've already know a lot about Grey Wardens and have had several as companions, unlike the chevaliers. (But there's a chance Blackwall was a chevalier before he became a Grey warden, so that would solve that problem!)
Honestly, I think it would have made more sense if the Inquisition's military advisor were a chevalier instead of Cullen... As much as I like Cullen and look forward to romancing him, he doesn't really strike me as a military strategist. I mean, the Templars are really just glorified prison guards for the mages, so being the "Knight-Captain" isn't all that impressive in my opinion...
I would always give them a chance to explain themselves, like I did with companions like Sten and Zevran. After that, I will enact what I see as proper judgement. If said Chevalier companion was similar to Dorian in the "I hate what my group has become" and regrets their actions, I wouldn't kill or imprison them. But if they are approving of or even meh on what the Chevaliers do, I wouldn't hesitate a second.
Sten killed an entire family (including kids!) because he was upset that he lost his sword and once you get to know him, he doesn't hide the fact that the Qunari will soon invade, killing any innocent person that doesn't convert to the Qun. And yet you let him live?
And Zevran LOVED his job - he enjoyed killing countless people for money. Sure, some of them may have deserved it, but how does that make it better? He was still a mass murderer.
And yet you balk at the thought of a chevalier who kills a city elf as part of a traditional initiation rite?
I doubt most of the chevaliers enjoy it (that's probably why they get drunk to do it) but it's expected of them and helps them bond and become a band of brothers. What if they secretly regret having to kill city elves but are ardent in their belief that the chevaliers, as a whole, are a respectable group that help a lot of people and do good? Would you let that potential companion live?