Is it such a bad thing to think that humans may actually turn out atleast ok, and have a good future? There can be a balance between Star Trek's humans and a more realistic approach. B5 isn't it. B5 takes it about as bad as it will go. I personally don't like that route. In the end, it doesn't really matter. In my head, the episode is not in continuity. Much like how I ignore the TNG episode that hobbled the Enterprise's speed (presumably because the people in charge were taking stupid pills) or that a lone ship in the Delta Quadrant broke the Warp 10 barrier, I'll pretend that humans don't revert to the dark ages, and that the whole episode just doesn't exist.
Humans turn out more than ok in the B5 future they eventually "evolve" into energy beings with incredibly advanced technology able to blow up stars on a whim while riding in organic spaceships.
The "great burn" is just a minor setback that doesn't really ruin the grand scheme of things for humanity all that much since the off world colonies and other places were not affected, that and humans from off world like the rangers were willing to donate their time and help the survivors advance and rebuild and not resort to a "too bad so sad, I've got mine" attitude they could have adopted but didn't.
You act like the dark ages was permanent and the human species goes extinct or something which simply is not the case.