The thing is, if we believed that was the only solution then we wouldn't have offered to help her find another. And the shards can be rejoined. The Ancients could be restored except that we're currently using their parts. Personally, I'm not down for returning them, but I can still understand why the Ascians decided to play repo man. And that's exactly how we acted. No effort to find any way of sustaining them that wasn't harmful to us. We just declared them malformed creatures and hit delete when the only thing that kept us from trying to help them was their leader wouldn't cooperate.
The Endless aren't about to destroy people. If they were, sure is weird how we're putting on plays for them and buying them ice cream. No, Sphene was about to destroy the Source for them, the same way Varis was willing to drop a moon on us for Garlemald but I doubt anyone would advocate wiping out the Garleans so he'd have no one to fight for.
Again, your insistence that the only way these people can be sustained is through death flies in the face of our offer to help her find alternative means. That offer means the Scions believe there are alternative means and the universe has other immortal beings that don't require life force to exist.
If killing the Endless was a terrible act we had to do to save ourselves, why did we go on boat rides? Eat popcorn? Visit a museum in the middle of these grave and terrible acts? Also the hope was she'd stop if we took them all out as she wouldn't have anyone to provide aether to, but she didn't stop, we had to kill her to stop her, so deleting the Endless was pointless. We could have left them as is and they would have remained in the system if something destroyed them, giving us all the time in the world to find a way to preserve the ones that wanted to be preserved, even if they weren't people (which I don't believe), we casually deleted swaths of their history and culture in expansion that espoused the importance of working together for a brighter future and appreciating one another's culture. Oh, the irony. We even deleted a museum with information on our own history that's not known on the Source. The last zone is embarrassing.
It doesn't matter how far gone Sphene is because we beat her to death just like we beat everything else to death. We've gone to the edge of the Universe and punched despair in the face, deleting the Endless in no way impacted our fight with Sphene. Either we punched her to death or she was gonna drain the Source anyway. Erasing the Endless had no impact on the outcome. We thought it might dissuade her, but it did not. And imagine erasing an entire people and their history on the grounds that it might discourage their leader. Yikes.