At the end of the Built to Last quest, it's revealed that creating Forge Knights involves binding stolen souls to them. Because I have Benvolent-3, Dunstan comments that he's surprised I'm okay with it.

 

Well, I'm not okay with it! But there doesn't seem to be any option not to go ahead with the plan. Is there an alternate resolution I'm missing?

I was wondering about the exakt same thing. Came here after searching for a thing I might have missed. I retrieved the notes but Dunstan only takes them with above comment and Clyver has no more dialog. Dunstan even comments that he disagrees with the plan so I hoped there was a way of destroying the research notes.

Well, you could just not turn them in (or reject the quest in the first place)....

 

Note that this isn't a critical path quest -- you can still advance in the game if you don't help the Crucible Knights.

There's only one way to successfully complete the quest -- if you don't want to do it then you'll just have to leave the quest alone.

 

Bear in mind that in the follow-up quest, Winds of Steel, you do get the opportunity to make the choice.