Oh my! Such a heated debate. But this game really brings it out - I've definitely ranted enough on my own time with friends about some of these issues. But just to throw in my two cents:
The Arishok: I have respect for the Arishok. Not because he's a big guy with a deep voice and an 8-pack, but because he's very principled and disciplined, as the Qunari generally seem to be. While Qunari values are radically different than the ones we've been exposed to among Fereldans, Kirkwallers, the Dalish, and the sprinkling of other cultures we've seen in the DA universe, I think it's a bit too easy to dismiss them, and the Arishok, as mass murderers. Certainly the Arishok was willing to go to war with Kirkwall, but he earnestly believed that he was doing so as a matter of moral and ethical obligation. He believes unwaveringly in order as it's defined by the Qun. Does that mean he was right? Well, not in my opinion, and not in a lot of other people's who hold typically Western values. However, I do have to respect the fact that he is principled. He sticks to his guns, he fulfills his obligations, and he protects those in his care. He's actually a lot like Sten from DA:O, and I think Sten from DA:O would have wholeheartedly supported everything the Arishok did, right down to the single-combat battle to the death. Of course, people who hate the Arishok might not have liked Sten much, either, but honestly, there aren't that many military or political leaders, especially in Thedas, who haven't gotten their hands dirty - in fact, even King Alistair, whom is a pretty decent, ethical guy, could probably bathe in the blood of the people he's personally - nevermind what his army has done - killed many times over. The Arishok is just straightforward about it, and holds a worldview that's really quite alien from the Western philosophies on which the Fereldan and Kirkwaller ethics we've seen so far seem to be based. We also don't really know everything about the Arishok - in one of the codices, it talks about how the army is only one part of the Qunari's larger body, and that going to a Qunari city is necessary to understand the whole. I really, really, really, REALLY hope Bioware lets us do that, because I think the Qunari represent one of the more fascinating cultures I've seen introduced in a fantasy universe, like, ever.
Meredith: Oh, Meredith. I think it's hard for me, at least, to really talk about Meredith and her merits because from almost the beginning of the game, she's starting to be lyrium-addled, and only becomes progressively more so as time goes on. I mean, we don't get many indicators of what she was like prior to the Deep Roads expedition, but it's plausible that she may have had a bit of an addiction to it even before then, given what we've learned about the way the Chantry keeps the templars in line. But that's just speculation. What we do know is that the lyrium idol that Meredith converted into a sword be makin' people cray cray, and cray cray she surely was. I'm not sure what the arguments have been in support of Meredith because I've been fairly insulated from player/fan discussion until very recently, but just to start, Meredith's ideas that every mage has to be locked up in his or her cell and confined strictly to the Gallows is really oppressive. I honestly can see the point about mages posing a danger - they can and sometimes do. (Though I think the way the game handled portraying this was problematic in a number of ways, but that's another post, another topic.) However, they were essentially running an interment camp where everyone who even possessed the potential to do harm had to be locked up. The problem with that is that by that logic, human, elf, dwarf, and Qunari in Thedas should have been locked up, because I tell you what, they've all done pretty ****ty things, and without the excuse of being possessed by a demon. Meredith's extremism was very biased and not at all ethical, and the Chantry's tacit support of it was really unforgivable given the principles of the Chantry as an organization meant to be spiritual and beneficial to sentient life in the world. So I don't really get supporting Meredith, especially since in the end she really revealed herself to be a total crazyhead.
Anders: Anders - oh Anders. You break my HEART. In my first playthrough of the game, I avoided spoilers like the plague, I was so excited to romance Anders because I'd wanted to in Awakenings, but there'd been no opportunity, and despite his diminished playfulness and sense of humor (and his newfound temperamental personality), I really enjoyed his character. Even though she was a rogue, my first character was very pro-mage, given that her dad and her sister/bff were mages, and she was very supportive of Anders.
Until he committed an act of terrorism and mass murder, and not only that, lied to her to make her an accomplice to it.
And thus is the trouble with Anders. Whatever word we want to throw on it (I think 'abomination' is a really loaded term and despite the skew of the game, unfair in some cases), he was forever changed when he merged with Justice, and on the personal friendship/relationship level, there is nothing more important to him than his cause. That betrayal is extraordinarily difficult, in my book, to forgive, despite my character having been completely in love with him - friend romance, not rival romance - and having honestly been aligned with him politically, if not as radically.
As to the ethics of his actions, Anders' actions may have been an act of war, but we never got to see the other mages who were behind it. In fact, we were very much lead to believe that Anders acted pretty much entirely on his own, even if after the fact other mages might have been glad of it. I would say that the Chantry itself is difficult to categorize as a civilian target, but it's also not quite accurate to call it a military one. The Grand Cleric did have the ultimate authority over the templars, but there were also civilians in the Chantry pretty much whenever my party was in there during daylight hours. Beyond that, Anders did nothing but prove that mages were exactly what Meredith said they were. There was a lot of ineffective leadership that lead up to Anders taking the action he did, but that doesn't mean he should have taken it. But the large problem here was Meredith, which should have been taken care of by...
Elthina: Now, I don't think Elthina deserved to die. But for someone who'd been in the Chantry for 30 years and reached the position she had, she must have been mighty politically incompetent to have been unable to rein in Meredith at all. For all her mealy-mouthed protests that it wasn't her place to decide who was right, what she didn't acknowledge was that, at least as far as I could tell, Meredith answered to her, and in fact, she had every ability to prevent things from going as far as they had. Now, I've said before I think the way the game handled the mage problem wasn't as great as it could have been, but the fact remains that more and more mages in Kirkwall were turning to blood magic and demon dealing, as well as just turning away from the Circle in general, because of the continuous and ever-increasing oppression they suffered under Meredith's regime.
(Although personally, I think the Circle of Magi is a pretty unethical solution to begin with, and I don't buy this crap about mages being sooooooooooooooooooooo daaaaaangerous they need to be imprisoned. While against civilians this is true, the fact is, a well-trained templar can take down a mage of a similar level without too much trouble, I'd bet. In my second playthrough, with my first mage, during Night Terrors I mistakenly [and naively] thought I'd beat the system by bringing in Fenris, Varric, and Anders/Justice so that only one of my party members would turn on me and it would make the whole thing go faster. OH HUGE MISTAKE. After lowering the level to Casual, Fenris still handed all our asses to us FOUR TIMES IN A ROW, and generally in the span of a couple of minutes, even with my Mabari summoned. Though we could chalk that up to battle incompetence, which it might have been - I'm no expert, but DAMN, STILL. Two mages and an archer < one well-trained warrior [we killed the Pride demon in like two seconds, it was just Fenris that spanked us all].)
Anyway, Elthina was incompetent at best, probably almost criminally negligent of the well-being of the mages who were supposed to be in her charge, but honestly, even so, I don't think she was malicious, and I don't think she deserved to die. She seemed like a nice old lady. She shouldn't have risen as high as she did, though. An effective leader would never have allowed the Meredith situation to escalate to the point that it did. I'm surprised Divine Justinia didn't have her ass forcibly removed after Leliana reported back.