If someone like HP Lovecraft were writing this series then not only would your theory be likely, but the whole "TWG is a rebel Old One" theory be likely as well.
However, it is Jim Butcher writing this series and as much as he likes to play cons on the audience, I doubt he is setting up TWG as the villain. Aside from Jim's personal beliefs, as others have pointed out actions speak louder than words, and the actions on behalf of TWG seem to be far more ethical than those of Hell and the Denarians (which are not necessarily on the same side entirely).
The problem of evil is always a difficult philosophical issue, as there is no easy answer. The answer that makes the most sense for the series is that TWG is not all-powerful and therefore cannot deal with the Outsiders on its own. Anything else could imply a level of negligence or insanity or sadism.
Power restrictions are a constant theme of the series and I don't see why TWG wouldn't have its own restrictions on what it could do.
I agree with Snark Knight's theory on some of the possible motives of the Denarians, and that the cause of the War in Heaven and the Fall is largely to do with the Outsider problem.
Shift8, the ends justifying the means is a very dangerous philosophy. As is utilitarianism. They are not to be treated lightly. Many leaders who thought their actions were right embraced these ideas and often became the worst dictators and monsters. Which isn't to say those philosophical ideas are entirely devoid of merit either, it's just that they must be balanced with other ideas.
For instance, you say that the Denarians might believe that any means necessary to stop the Outsiders win is acceptable. Mab also may believe this btw, based on some of Jim's comments. But the problem with say, torturing Shiro to save the world is that poor old Shiro still pays the price. Should Shiro have to eat dirt, unwillingly, so that we all might benefit? He might choose to sacrifice himself (as he did for Harry), but was he told his torture would save humanity? Did he get a choice there? Could the Denarians have achieved their goals around saving Earth from the Outsiders without torturing Shiro? All legitimate questions.
So no, I don't yet believe that TWG is the bad guy. But I will say it would be an interesting series, in another series perhaps.
It reminds me a bit of His Dark Materials, God (called the Authority) is actually just the first Angel and lied about his deity status (although he is very powerful). Another Angel later (called Xaphania) discovers this and leads a rebellion. It is initially unsuccessful and like the Fallen in most stories they stay in conflict with Heaven. The Church is also generally evil, and the Authority is a tyrant. Also contains a multiverse in that series, but only one set of Angels. The world of the dead is a prison camp for souls. And there are weird Outsider-esque monsters called Wraiths. It's a fairly interesting series mostly told from the point of view of children, although the story can be a bit slow at times. They made a movie out of it (which wasn't very good) although the new television show seems better (I have only seen the first episode but it seemed much closer to the books). Worth checking out the series in one form or another if you like those kind of flipped ideas.
