What constitutes something as being "alive" in XIV lore right now? Are the beings in the Ultima Thule alive? Are Omega and Alpha alive? Are primals alive? Memory seems to have been established, in the msq, as a real, physical entity, that we can see (visually, the orange orbs) and interact with (can be manipulated and stored in some capacity, not sure if physically or like energy, but matter and energy usually end up being the same if the world has any semblance of physics). The beings in the Ultima Thule are the result of Meteion's memories and Dynamis powering them up. Are those alive? Omega wasn't designed, as far as we know, with a soul. But, at some point in time, it started to think, and feel, and question its existence and its place in the cosmos. Is Omega alive? If you were to split a being's self by separating "memory" and "soul" and destroyed the memory part- is it alive? You're claiming the reverse is a categorical "no".
I'm not even saying the Endless were truly alive- I really do not know. The game sometimes says and acts like they're not, and sometimes it acts like they are. My sentiments are that it's a "maybe"- not that it mattered, I had to destroy them to save the Source. But I fail to see where the convincing evidence that they were not alive in any capacity is beyond "oh, we were told they were just AI, and AI can't be alive". A person isn't the prison of flesh, it's the electromagnetic pattern that forms their mind, in my view. And that electromagnetic pattern could, hypothetically, be stored in a machine.
You're conflating two things.
One is: "the endless' existence is incompatible with life on the Source and, therefore, they had to be destroyed to preserve the Source". Yes, correct. There's no argument there.
Then there's "the endless were not alive, so destroying them has no moral consequence". This is not evident. Maybe they weren't alive, and were just simulations. Maybe they were alive though. And the game doesn't seem to be showing me that they were lifeless, robotic AI, especially given how they diverge from their original settings on a whim. In fact, the story is better if there is a moral consequence to our choice. Was the WoL justified? Yes, it was for the survival of the Source. But doesn't make it less tragic. Unless, well, you posit that they weren't alive because "AI", which is where this started, isn't it? It doesn't even matter that they're AI, anyway. If a living army of aliens showed up and needed to exterminate life on the Source to sustain their existence, the WoL would still be justified in killing them as an act of self-preservation. That isn't even the point of the discussion.