Makes sense, I thought it was cool that the dev included that choice. But now I realize it's more of a false choice, as killing is not really rewarded, rather it's detrimental to the experience. Would be nice if that play style was also supported, like killing characters would unlock certain content and give you access to even more characters to kill, then again character models and sex/killing animations don't grow on trees so it's understandable.
Look at it from different angle - limiting choices force you to seek alternatives, to improvise.
For example, you can kill Rhyll (the mercenary guy) instead of recruiting him or using his help. That forces you to reach for other options, because you still need troops. Or you can kill Darja, locking you out of Spire lair option. Or Marie-Ann, which would lock you out of the lair in the Mines.
When decisions lock the content without reward, the change in situation could be a reward in itself. Limits lead to non-standard decisions, which enriches gameplay.
Besides, some people just want to have options to deal with certain characters. And this game gives you options to deal with almost every single one of them - in many different ways. Ignore, cooperate, befriend, enslave, destroy - you can do at least something with every character you meet.
The amount of branching decisions is stunning. Even major, story-significant decisions aren't few. It leads to insane replayability.