This is a tough one. It kinda contradicts with the other missions' alternative options. Yes the twins can be send to their own coal mines instead of being killed but doesn't that serve the same purpose? I mean, it's poetic justice and all and technically they don't die but you get rid of them in the long run. So that's a mission success. So, if the people who are helping you or whatever don't want you to kill him, what could happen? Maybe they will script some dialogue while you're walking with him and he starts tempting you into killing him?
There are a lot of interesting ways they can go with that. What if you can threathen the twins in The Golden Cat level? You don't kill them you just display your raw power and they offer you a deal. That can be awesome and it can affect the story later on. There are a lot of game desing ideas that always go into a game like this. For example, if you kill the doctor, he might have been a bastard but he does save lives. A couple of innocent people die because of it and your Chaos increases, thus changing the world around you.
There are literally a ton of options they can go on, but once again I am afraid to go with the development time card. It's really a big issue. I have only worked on one title and I was brought pretty late in the development process and I still found it a giant pain. I have a lot of developer friends and when I ask them about their work they, for the most part, feel like changing the subject. I always ask them about a game that resembles real life events and the randomness/chaotic events that occur and how hard they are to program. It's really hard, even for minor things like the ones I mentioned.
With all that said, I really like the way you think but I am pretty sure that topic has been discussed when starting work on the game. We need an answer from a developer to see what they decided on. If it's like Thief and you break one rule of your mission assignments, it's Game Over. I always want to encourage developers to make gamers learn from their mistakes and not issue the Mission Failed screen and calling it a day. There is also the issue of the story aspect in that, is Corvo really going to do this? We need to know the character in and out to be able to do this option. That is speaking within context.
Like I said at the beggining this is a tough topic and I am sure we can discuss it endlessly. I really like the idea and I have had some thoughts about it but I wouldn't keep my hopes up unfortunately.