They absolutely had to be stopped- it was a "us or them" situation, and killing them all to save the Source is justified.
The problem is how this is presented ingame, and you actually touch on the dissonance yourself with your post.
These entities are shown to be sapient and feeling and creative. They do things spontaneously, they love, they have regrets and dreams, they're very much self-aware. You explore this in the quests in the area and the game seems to be showing me that while the circumstances of their creation and the medium that holds their minds/selves is different from mine, they are capable of thought and feeling all the same.
It's therefore tragic that their survival requires my death. I wanted to see more conflict about this, more despair, more vainly trying to attempt ten things to avoid this outcome before finally bringing the axe over their napes down. I wanted to see the WoL and the scions feeling conflicted and heartbroken over this- and maybe this is a thread that can be followed up on in later patches. In that moment, the WoL could maybe really feel like they were wearing Emet's skin, and understand the gravity of the action. But this is merely brushed aside.
I also don't like the "aether vampire is bad" angle. All non-plant life requires death to sustain itself in-lore. Even a grazer will kill plants for sustenance. I am obviously not suggesting there's anything morally wrong with eating vegetables. The point that I'm making is that what you need to consume to survive matters a lot. If a creature needs to eat carrots and another needs to consume dogs, I can see someone being squeamish at the latter and ignoring the former. Here, we have an extreme version of this- they need to eat us, with the aggravating factor that they have no natural population control (for better or worse, people die in Eytheris all the time, otherwise resource exhaustion might become a bigger problem than it is already). Therefore, the real issue is that our existences are incompatible. That's why we need to kill all of those thinking, feeling creatures. That's why it's tragic. I definitely did not see it as a "mercy". I saw it as a tragic fight for survival by two inherently incompatible life forms. We were justified in our actions, but we killed living, thinking things all the same. That wears you down, emotionally. Or it should... but DT being DT, this is going to be forgotten, if I had to put money on it.