You didn't kill Alfira (light spoilers)

[Doppleman]

Playing the Dark Urge and got in that cutscene where you allegedly killed Alfira. You didn't :p
So after that cutscene, I cast speak with dead on her to try to figure out what actually happened. Somehow, none of the questions are relevant.
But then, later in the game I found out that the deads don't want to speak with their killer, therefore you are not Alfira's killer !
Ok, that's just a random theory, I didn't finish the game and I actually don't know what's going on with the Dark Urge memory loss. Still, I think that's food for thought.

I also checked if that was due to Alfira, maybe, not being aware of getting killed so I tried killing people while sneaking and the spell just didn't work on those, so I couldn't confirm if being an invisible killer would change a thing.

[Passionfruit]

Some dead won't speak to their killer, others will.

[Gracey Face]

They seem to have abandoned that "The dead won't speak to their killer" thing as they went further into the game. I am in act 3 right now and can't think of a single corpse I killed that would not speak to me.

[Adam__86]

The dead won't speak to their killer

Isn't consistent

[Seva]

You can knock her out before you sleep at the camp and trigger the cut scene, a replacement will show up in her place and you kill them instead of Alfira.
Edit: a bit off topic but i think it is relevant.

[Tomas Mac Mordain]

It's not a deep secret you've just uncovered. Just an inconsistency - looking at the track record of ways to break quests etc. it's much more likely. They did not put that kind of level on detail into the game. It's not Dark Souls levels of layered lore. It's just 'content production'.