But he also could have died depending on if you killed him . so that wouldnt make sense.
Canon>player choice.
If canon says that Desmond did not die then he did not die.
Doesn't matter if some people killed him, they got the choice to kill him during their playthrough, but if in the official universe/story/lore he did not die then it doesn't matter if people killed him.
An example, Marcus died for me when I tried to clear out the Tanker in San Fransisco, yet in Jacobstown he is.
I didn't rescue Tandi from Khans and yet NCR was still born and she still survived.
What we as players did don't mean crap when it comes to the official story.