The bottom line is that what Anders did was reprehensible. It was murder, without question, and the murder of innocents is NEVER justified. Having said that, it is also completely and utterly true that the kind of change he was advocating for would NEVER have happened otherwise. There's just no getting around it: in the real world you see example after example of drastic, permanent changes being made in the world for the GOOD. What nobody ever likes to talk about is that good people, innocent people, can and DO die in the process. The point was also made fictitiously with Andraste: she threw down the Imperium and freed the slaves, and created the Chantry. But she was also a conquering warlord. People DIED because of her, and not all of those people were servants of the Imperium. Many children and innocents died.
As much as I hate what Anders did, I have to agree with this. Drastic changes aren't possible without drastic measures. And that means that many innocents will get tramped underfoot. Damn. Anders at least was honest enough to recognize that and submit to your judgement (hell, you could make him kill mages for the Templars, in an incredible twist of events).
Andraste is a very good example, now that you mention it. Let's imagine a game set in those early days.
Tevinter was THE civilization. If you wanted law and order, it was Tevinter or nothing else. Of course, those in charge abused their powers often, but every system has its faults, doesn't it? Ok, there was a Blight that weakened it, but you can always count on the Grey Wardens to save the day. Oh, yeah, those elves are asking for their freedom and accusing us humans of stealing their culture and immortality. Bigoted extremists! But there will be always some nice magister that will want to change things, so wait and let them work.
"Oh, no! Barbarian hordes are marching against the empire! They're waging unprovoked war against the seat of human civilization, killing women and children, and stealing whole chunks of land! Worse, they're leaded by a religious extremist who claims God is talking to her to bring down the empire! If things keep going on this way, all of Thedas will be conquered by this madwoman and her foreign religion will be imposed by force on all of us!"
I wonder what we would do if we could play that game. Without hinsight knowledge, of course.