It was my duty to protect Emily, and if you tried to stop me, then you deserved what you had coming.
At least, that's how I rationalized it. Havelock and the others told me this was about putting Emily on the throne, to have a true ruler in Dunwall. I didn't care about that. My only goal was to make sure Emily was safe, and I would take out anyone who threatened that safety. It didn't matter if you were a weeper, guard, or the Lord Regent himself.
I stabbed, shot, and sneaked my way through dozens of guards to rescue her from the Pendelton twins, and I did it again after the admiral and his comrades attempted to rid of me. The Empress had given me one task, and I wan't going to let her down or Emily down. So when I reached the top of Dunwall Tower, I didn't hesitate: I put that bolt through Havelock's skull within a second.
I ran over and pulled her up from the edge. It was over. I had saved her, and no one could ever do this to her again. She was safe.
"The others are all dead, aren't they?'
I felt a slight jolt of regret, but I knew I did what had to be done, even if it meant Emily would no longer look up to me. It was worth-
"That's alright, because I was going to have them killed anyway."
My stomach dropped. I took my hands off of my keyboard and stared at my TV. The epilogue was playing, but I didn't care about that. I had fucked up. I thought that I was protecting this girl, but all I really did was corrupt her. She had looked up to me, and I failed her. I sat in my chair, thinking about what I had done. A few minutes later, I had started up my second play through of Dishonored. I wouldn't fuck up this time.
I think what made the exchange between Emily and Corvo at the end so effective (at least for me) is the way Dishonored handles morality. The effects of how you play the game are shown through the world and the characters, instead of on a meter. Often, it is small things, like the number of guards in a certain mission, or the pictures Emily draws for you. It's this attention to detail that makes it really feel like you are affecting Dunwall.
The way you make choices is also important. You're not just selecting options from a menu. Most of the time, you make important decisions completely through gameplay. Have to get rid of Lady Boyle? You could simply kill her at the party, or you can knock her out and give her to a man who claims he is in love with her. Any way you handle this situation will be done through the mechanics of the game. So when you get to the end, and Emily says she would have killed those who betrayed you, it feels like you caused that through the way you played, instead of some arbitrary choice near the end of the game.
The ending make me feel like shit, but I deserved it. Through my slaughter of all those innocent guards, I had shown Emily that it's okay to do horrible shit, because the ends justify the means. My actions directly affected the way the future Empress thinks about the value of human life. It's honestly refreshing to have a game tell you "Hey, you might not have thought about it, but you're kind of a mass murderer. You can't act that way without some repercussions."