Seems we learn more as we go on karma spots that he could have saved, but didn't, and we see the consequences of his choices where it still plays out the way it had in the first timeline when he was a hunter. Pretty sure it's just karma stacked against him that resulted in the punishment, but we can see that he can fix it and take down the evil organization as we go.
It's a common path when faced with multiple routes. Just because the path is well traveled that you've decided to take doesn't mean there isn't hidden karma points that can be a benefit for you, a harm in your future, or just nothing if you miss it. It's a nice play into the plot to make the story interesting, so I'm looking forward to how the sticks fall for this story.
Ok, this might be a hot take here and controversial but I feel the punishment he got didn't really fit the crime? I just started this but I'm a bit bothered by the general attitude towards him. Other than the cleaner incident, do we see other instances of him harming people? Sure, he's a dick, but all he actually did was shove the dude, after being grabbed first. I understand that he's significantly stronger than the average person so that would really hurt the cleaner guy, but MC was literally the number 1 ranked in the world, routinely risking his life in the dungeons. If we take other hunter stories as references, S-classes were often solely responsible for stopping entire dungeon breaks and now this dude who was humanity's first line of defense is gone and that's a good thing? Regardless of his attitude, unless he did some seriously f*ed up shit (aka. Flame Emperor) on the level of killing civilians or r*****ing people, it is completely stupid to kill him and condemn all the people he would have saved. I honestly don't get the reasoning.