There are several common problems that occur in games with sin/karma mechanics. One is that you can be considered an evil demon for only doing a tiny little sin, if you do it often enough. Say your character steals an apple, and thats worth 1 sin. Fine. But you steal 100 apples, and suddenly you're considered the most evil being imaginable, even though you've never hurt anyone or done anything else bad at all, you just stole apples.
So for this game, different kinds of sin are treated separately. If you steal once, you get a tiny amount of thief sin. If you steal constantly, you gain thief sin for a while, but then you stop gaining anymore. By that point, it's obvious that you're a thief. The game remembers that, and you don't get any more sin for it.
Each 'bad' act is only able to give you so much sin before it's considered part of your character. If you kill a monster once in combat, that might have been an accident, that doesn't make you a killer. If you kill dozens of monsters, you're probably the kind of character that wants to kill things.
Stealing, striking the first blow, being a bully, killing animals for food, killing for fun/profit, murdering the helpless... All of these things can end up as marks on your character. So even if your overall sin is low, if you are clearly a thief that might affect your ending.
The other problem in games with karma is that you can be a horrible evil murderer but get off free in the end because you gave apples to orphans. Which is why in this particular game, sin is very hard to get rid of. If you murder someone, you can't make that better.
And no, it probably wont work the same way in the sequel (assuming there is one). The point's been made, there will be a different point next time.
