Do I hate Anders? No. Did I let him live? No. To dislike Anders for how he was and what was to follow is to not take into account the actions of what would be many many generations of people. The problem started when Maferath betrayed Andraste. With her gone her followers became like the very evil they were fighting against. The Chantry just doesn't use blood magic to control the minds of their followers. They use religion, and Lyrium. Does Anders get on my nerves during the game sure, so does pretty much all the other companions especially when they betray me in the fade. I mean doesn't leave me a lot of confidence in them having my back afterword. What if Meredith had of offered Isabela her own boat as an example.
The Chantry were moderates in all of this.
The original hard-line mage hunters were the Inquisition. A seperate, more hardcore Andrastian faction. They hunted mages indiscriminately. The Chantry, if anything, chilled them out. They created the Circles to protect mages, and thought it was wrong to kill them like that. While at the same time, got the Inquisition under their control and focused their anti-mage efforts to become Templars, with the job of both protecting people from dangerous magic, and protecting mages themselves. It was supposed to be a win-win situation for everybody.
And it was a win-win for millenia. Millenia. Hardly anything works for 2000 years like this did. I'd call it a success for the most part. Not some failure from the get go, "starting with Maferath". It only became a failure when you invite mentally retarded spirits like Justice into the world. He doesn't understand the concept of "process", balance, or compromise. Which are essential to REALITY... especially social and political reality.
Nobody is going to come up with a better solution than this original arrangement. And have it last as long. The only thing Anders has done has caused chaos. No actual problem solving.
edit: I'll add though that the one Chantry element that has failed it's duty is the Seekers. Not people like Elthina. Part of their job was to keep checks on Templars. To stop abuses. Which they didn't.. they became too sympathetic to Templars instead. This can be fixed though. And you don't have to blow up people to do it.