Another Babylon (Spoiler!) Question...

From what we know from Nasu's notes and the like, the CONSEQUENCES of what happens in the singularities have meaning and impact on the epoch as a whole in question, not the literal consequence of people staying dead if they die in said singularities (though this happens too, and I am pretty sure we saw Gil's actual death in history for example, at the end of Babylonia, among many others). There are of course, also exceptions to this rule (when are there NOT exceptions in Nasuverse lore, haha), such as Camelot as a whole and much of what happens because of real Tiamat's actions in Babylonia.

Think of it as "the damage done in a singularity is not to "that year", but "that era", so there's a plus-minus to the calculations. As Gil said, at the turning point of an era that has become a foundation for humanity, if the pluses increase, so do the minuses", according to Nasu's own words. In other words, as Gil says, there is always a sort of balancing for what happens, it doesn't all just get erased, it's a kind of equivalent exchange. It's an interesting compromise, though I do think Nasu is stretching it a bit, but convolution in Nasuverse lore is nothing new, and I get what he's going for conceptually here.

Basically, Gil dying is fine because he was fated to die here, this is the end of his legend, and also him acting as the key to the transition to the Age of Mankind and the end of the Age of the Gods. He both accepts that he has die for this, but also fights fate to even ALLOW for an Age of Man, which fittingly makes him mankind's oldest and greatest heroic figure. Uruk's first dynasty falls regardless, but we did enough to allow human civilization in Mesopotamia to thrive beyond this, and history can now correct itself onto the right path before Solomon screwed everything up. Gilgamesh played his role, and did enough to separate from the gods, that's the whole thematic point of Babylonia. Him dying doesn't mean our mission wasn't successful and history wasn't corrected, ultimately.