This is something I aways notice when it comes to the DA fandom. That players many times will overlook our companions crimes and mistakes mostly just because they are our companions. Because let's face it, if they were mere NPCs rather then our companions, most players wouldn't think twice before throwing an knife to their faces for their wrong doings. And in some cases they will even try to justify them.
So I wonder, if in Inquisition one of our companions were to do something that normally we would find outrageous, would you punish them for it just like you would for anyone else, or would you let them get away with it because they are one of your companions?
Who is this "we"? For the most part, I don't "punish" my friends in real life for doing things I find outrageous. Granted, my friends in real life aren't assassins and thieves, but I'm also not trying to save the world from a disaster of epic proportions. Nor are my friends constantly under threat of OTHER people killing THEM. So I'd have to say that even my personal reactions to borderline behavior would probably be substantially different in those conditions.
That being said, I executed Anders for blowing up the Chantry. His actions were unconscionable and he showed every sign of having become dangerously insane. Yes, mages are oppressed. Yes, the Chantry is in large part responsible for that viewpoint (although the mages themselves have done a fair job of encouraging that belief all on their own). But doing EXACTLY what you're oppressed FOR doing in retaliation to that oppression is hardly the way to convince anyone that mages should be left alone. "Oh, you don't want us to blow people up? I'll show you how wrong you are! BY BLOWING PEOPLE UP!!!" Yeah, no.
However, for a contrasting example, I did rescue Sten from the cage and even went so far as to track down his sword for him so he could go home. Yes, he was a brutal murderer, and that's not the kind of thing you can come back from by just saying "whoops, my bad". I have serious reservations about anyone who could even stand to live with themselves after doing something like that. But that's the thing--he was TRYING to die. He did everything in his power (other than actually slitting his own throat) to see to it that somebody had the opportunity to take his life for his crimes. He even tells you to leave him be. The only thing that perks him up is the idea that by coming with you, he might actually get a chance to fight some darkspawn and die with a little more dignity and some semblance of honor (by the standard of a Qunari soldier, anyway). Yeah, I turned out to be a badass and that whole death thing didn't happen, but I figured, he at least earned a second chance for himself by then, so I said goodbye to him in a hopeful frame of mind, if not without some reservations.
So, long story short: "It depends". Morals don't exist in a vacuum--you have to *think* to apply them to a given situation and take in the *whole* context of that situation. You don't just plug a few descriptors such as "murder" into a mathematical equation and get a "how you should respond" answer out.