Alan gets his bad ending in Ark but he shows up in the sequel. You'll see something surprising.
To those who got confused about Esil. She's a demon king's subordinate. Therefore, she's probably just a "remnant" or a memory of Baran's army since Baran was already killed by Osborne in the Chaos world. Esil is a soldier and her family is a low rank, therefore they would have been dispatched earlier during the war in Chaos World. The fact that Baran got killed means those at the frontline died first. They were just probably made by the Architect.
The MC is someone who cherishes life, humans and his soldiers as well. So his decision at the end was true to his values and he indeed made the most easy decision for everyone but hardest on himself. The sides stories would help others to understand more but personally, if you're immersed to the story and know about loss you'd get his decision right away. Osborne respected that part of the MC because they both had unwavering loyalty and love for the people around them and self-sacrificial.
I respect how the author stayed true to his character's wishes. Jin-woo chose a life where people didn't have to lose anyone due to the gates or to the eternal sleep. Even if he chose to continue after, the loss and grief would have been immense. Normal people would still continue to die after the war since only Hunters are able to adapt in the new earth.