Honestly, i haven't read the entire post yet so I'm not sure if these points have been made yet, but here goes.
The first point I'd like to make is alot of the draw to the game is that there is no "good" faction just like real life. Good itself is a relative term that is subject to opinion. (For give me for the historian babble that follows I'm in school to become a history teacher ) Take any war from time. Both sides no matter how wrong they were to our own ethics honestly believed in their cause and thought it to be the "Good" and "Just" way. Never mind the thousands of innocents that were killed in the process. The next point is the factions involving the church. Honestly the guild already seems kind of churchy to me. Just the whole witch/necromancer/demon hunt really reminds me of the catholic (menoth) faith over the various eras since their creation. Not to mention i wouldn't in the slightest consider a church faction to be the "good" guys. I understand that a religious faith tends to bring to mind shining crusaders of good, but even evil can have paladins, Albeit with slightly different powers but Death Knights from wow, or dark knights from the final fantasy series are fine examples in my opinion. (Once again excuse the history babble) Not to mention history shows that the church has committed quite a few murders in its time simply not to loose power or gain something they want (Joan of arc, as close as well get to a real life pally was burned for being a witch simply because she was a woman who claimed to be able to talk to god or the crusades where they suddenly decided they wanted to own jerusalem. Among many more). Finally, its a skirmish war game no matter who you field they are gonna be killers and mass murderers. Its just the nature of the game. Sorry if I was blunt I just couldn't hold that in. Don't get me wrong i would love to see a new faction in this game and I do find your ideas thoughtful and interesting (the amish preacher would be a riot) i just don't think a "good" faction ever really works.