I have yet to complete the absolute newest version of TLS so if there is an added consequence of this choice later on, I'm unaware (and I don't mind being told if there are).
At the end of the Erosian War, you get to decide Estaven's, aka The Fucklord, fate. Wendis yoinks his soul in the Tower before he passes and you then have the choice of offing him immediately or making him relive all his rapes but as the victim, whilst his soul is shredded to nothing. A fate well deserved, as Estaven was a selfish obnoxious pedophile who had zero redeeming qualities. The Incubus Emperor, in my opinion, was at least funny in how cartoonish he was.
Of the guides I read, they all suggest the goody two shoes option, believing that there will be a consequence to this later on. I have faith in SL that the option is not so simple as BAD CHOICE vs GOOD CHOICE.
I believe having him tortured is actually a good thing, if not just for the player's satisfaction, but for Wendis. You gain a massive 10 entity cohesion for doing so along with a point toward Sabitha. However, what's interesting about this choice is her dialogue afterwards. She tells Simon that halfway through she realized she didn't really enjoy it. This is vital to her mentality imo. She experiences what it's like to take revenge, but feels it did nothing to satisfy her. I think this actually powerfully works against her desire to destroy everything, moreso than just exchanging words with her about why she shouldn't, as she now experienced for herself what giving into that desire brings. Plus I suppose it serves as another vent of her hatred as we saw when it was unleashed on Simon.