I'm afraid time won't heal the villagers feelings in regards to non-returning companions, but this is not a bug either, it's just a way it is, and I'll move the thread at suggestions.
Adding mechanisms to tell the NPCs what really happened is tricky, and still even if the companions would die fairly I don't know if villagers still should always be like "He died when hunting with you? Ok, we don't mind that, here have a another hunting assistant, we wish him better luck than the previous. Hehe."
This is something to tweak/ponder in the future, but there's not an easy way to find a good consensus.
I'm still very newb on this, and am really just focusing on surviving the winter. I was able to find a village with a fine fishing rod.
Also, I'm appologize if this is an outdated discussion at this point, but I would like to contribute my two cents.
You guys already have a system of knowing where a person is hit and the types of injury sustained. Depending on where the injuries are located, and the types of injuries sustained, the village elders or shaman could have a chance of thinking that the player is in some way responsible, directly responsible, likely not responsible, or not at all responsible. That could of course be influenced by current reputation with the village. For example, if they basically regard you as a demigod hero, the Shaman or village elder/s could see a gaping axe-wound in the back, stripped of all gear, blood your hands and and axe, that your axe-blade fits perfectly the wound shape and size, his gear in your inventory, and still think it wasn't your fault, and maybe even have a chance of improving relations further depending on speech skills or something.
I like Saiko Kila's idea of requiring a quest to prove your innocence. If you're not actually innocent though, perhaps upon finishing the quest, you only manage to prove your guilt . . . unless of course the spirits really like you and are willing to lie for you. Side note on that. You could make evil spirits that tend to try and help evil players, perhaps while also penalizing them in other various ways. Perhaps if the player is evil for long enough, the evil spirits decide it's time to kill him for their own pleasure and send some kind of hellish beast after him that if he manages to kill it, they continue helping him, or perhaps it impresses the good spirits who then decide to give him an ultimatum, serve good or die for his crimes. If he decides good, then they send him on a quest for atonement first. Then they send him to a monk's sanctuary where he is to devote his life to good, learning to fight, and to serve the good spirits in various quests. If he refuses, perhaps the good spirits send one of their righteous monks to take him out, so he has a chance of still defeating him and remaining evil if the player wants to do that.
Anyway, off that tangent, that's all I have to say.