The game very explicitly implores the player to question the ethics of monster slaying -- most directly through the character of Djura, who points out that the beasts were once people too. The game goes so far as to give you a dialogue box when talking to him, with the options to spare the beasts or not
There is also the romp through the Hunter's Nightmare, whose first act is replete with beasts cowering in fear at the sight of the player character. Even if you spare them you'll usually see them brutally slain by mad hunter compatriots anyway
And it's no mistake that all the "kin" type characters you encounter in the game, like Rom, Ebrietas, and Moon Presence, are all deeply tragic.
Thematically Bloodborne is deeply concerned with humanization/dehumanization and how those interact with violence, and it plays a lot with this in the narrative to subvert with the usual power fantasy of the soulslike genre -- the beasts cowering in fear in the nightmare seem more human than the mad hunters, Ebrietas appears to be grieving when you encounter her, and with Rom you might systematically murder her children before directing your blade at her. Like you can live out that power fantasy, but it won't always feel great.
So no, I don't think that Ebrietas being optional works against this idea at all. It just allows the narrative to explore different facets of this question -- it humanizes her, and if you choose to fight her it's because you chose to be the aggressor.
Only in Old Yharnam! You're right to call it out, I missed that, but I feel like even the BSB in Old Yharnam has a backstory motivating you to put it down.
Arguably, not much in Bloodborne is even actually happening.
(My confidence on all this isn't super high, but this is like the one video game I do play, and I've gone a little deep on the lore.)
There is also the romp through the Hunter's Nightmare, whose first act is replete with beasts cowering in fear at the sight of the player character. Even if you spare them you'll usually see them brutally slain by mad hunter compatriots anyway
And it's no mistake that all the "kin" type characters you encounter in the game, like Rom, Ebrietas, and Moon Presence, are all deeply tragic.
Thematically Bloodborne is deeply concerned with humanization/dehumanization and how those interact with violence, and it plays a lot with this in the narrative to subvert with the usual power fantasy of the soulslike genre -- the beasts cowering in fear in the nightmare seem more human than the mad hunters, Ebrietas appears to be grieving when you encounter her, and with Rom you might systematically murder her children before directing your blade at her. Like you can live out that power fantasy, but it won't always feel great.
So no, I don't think that Ebrietas being optional works against this idea at all. It just allows the narrative to explore different facets of this question -- it humanizes her, and if you choose to fight her it's because you chose to be the aggressor.