That's the point. He's supposedly ruthless to his enemies, yet when such ruthlessness would actually serve a good purpose, the author bends over backwards to find an excuse for him to to stay his hand. Not only that, the excuse is exceptionally poor, as the decision is to the detriment to both him and especially Nell, since she'd never approve if she knew the details of how the situation was handled.Because Yuki was never particularly fond of senseless violence, nor making trouble for himself and his girls. The whole point is that while he has no major qualms about turning his enemies into mince, he's not a crazy berserker and doesn't want to become one.
Also, just violence wouldn't do much here. He's here to keep his wife safe and her honour as a hero intact. He can't rampage or use excessive force, because doing so would hurt Nell's reputation. He's also not at all shy to using violence in the last few arcs. I mean, guy literally tortured the enemy agent to near death and left him to be killed by a pissed off ogre.
Just to be on the same page: we were talking about events further down this arc in the LN. Have you read that far? I'm asking because I find it hard to believe anyone would defend that particular plot point.