Story-wise I think if he by any chance appears in DA:I, sparing him will have much more interesting results than killing him.
And on the topic of who died in chantry, it depends on what you think and see it. The scenes that game shows you only has the grand cleric and bunch of Templars in them and no one else, also it happens at night so i shouldn't be populated much. The explosion is also in the sky, dealing minimal damage to other buildings.
Anders himself never questioned that what he did was wrong. He fully acknowledges that his actions were murder, and were morally contemptible, and that justice was required of him for what he did, this act makes him much less of a hypocrite. What he understood is that it wasn't about right or wrong, it was about necessity. He believed that the system of imprisoning mages within Circles, under the watch of the Chantry's templars, was wrong, and would accept nothing less overthrowing this system. And with that, he understood that unless someone was willing to take drastic measures, then nothing ever would change, circles have been around for almost a thousand year and it is enough time and chance to wait to see acceptable changes, they never happened. He knew that the templars would rise against mages everywhere for his action, and that therefore all the mages locked within Circle towers would be forced to rise up against the templars in order to save themselves. By his actions, no mages would be able to take, say, Wynne's position that the templars and Circles are necessary, except for those mages who hated their own magic and wanted to embrace imprisonment or even suicide. They would have to either submit to templar tyranny, or fight to save their own lives. By extension, he removed the fake notion of peace (the grand cleric). Therefore he removed any stalemate--"there can be no compromise"--in the name of ending an indisputably broken system that served no one.
Also I'd like to point out that people like me who live in free countries should realize that we didn't become free with rainbows and chatter, our ancestors murdered, ravaged and looted so that we could have this life. So don't be so black/white when judging people like Anders, you need more shade of grey, a lot more.