This is a complex story so please try to stay with me here:
When you play through the quests in Markarth, you will encounter the quest "The Forsworn Conspiracy". This quest reveals that the whole of Markarth is corrupt and the Silver-Bloods actually run the whole thing. Since I have chosen Markarth as my home and sworn loyalty to the Jarl, I wanted to cleanse the city of the corrupt guards and such. I finally got the opportunity to do so by helping the Forsworn king Madanach escape the prison he spent decades in. When I finally got him, his allied and myself out of this god damned mine/prison, the forsworn went on slaying the whole guard and the head of the Silver-Blood family.
Now I have a clean, non-corrupt city in which I can live in peace but in the end I have slain ~20 guards who had kids and wives and I hear the constant mourning in the streets... I don't regret the whole thing, but I am now aware that things are not always black or white. Likewise in the ongoing war: Do I whish for a strong Empire that can stand up to the Dominion or do I protect that what the Nords now consider their home even though they took it with force from their predecessors?