I kinda feel bad for Hephaestus. At first he was just trying to do his job but then the stupid primitive monkeys kept destroying all his creations..... And no matter how he tried to compensate they just come up with new ways to kill them. Even when he started diverting energy from his main task to create machines specifically to deal with the pests they would just kill those too.... It's almost like dealing with the bed bug infestation where eventually you just get so frustrated you decide to burn the entire bloody House down.
Now if you think about it Aloy never tried to properly communicate with Hephaestus.
Minerva was unsure and scared to become part of Gaia again but in the end, she understood that it needed to be done.
Demeter, Aether and Poseidon were happy to return to Gaia. I loved how they referred to her as "mother".
Hephaestus was never evil, his main priority was building machines and keeping the terraforming system stable while Gaia was absent. He only became angry after he saw humans destroying his creations, by doing so Hephaestus deemed humans as a threat.
I believe if Aloy applied logic and tried to explain the situation to Hephaestus he might have accepted to return to Gaia