To be fair your not forced to be on the dark path even when you kill the assasin. My mc is usually rather good but i still take a few dark path choices (like killing the mentioned assasin).There are alot of choices and consequences in the game that make no sense to me but to others it seems perfectly reasonable. One of my biggest is the assassin scene. Light path you take his magic and weaken him (+1light, kill him +5 dark), he's still a trained assassin out for revenge who can strike from a distance and can hurt your companions or others. Why would you leave someone like that alive after they tried to kill you? If you kill him your going down the dark path for defending yourself and stopping a future threat to others. To me that doesn't seem like a dark path. That's like saying if you kill someone for trying to kill you or your family your evil. Doesn't mean I'm going out and killing people for the fun of it. Which is the more evil, killing a group of bandits or just beating them up and hoping they don't do it again?
With that being said while I don't always agree with the options available or consequences it is the Dev's story. My choice is to play it or not. If I like the story I play/continue on if not I move on to the next. Sometimes I point out things other times I just deal with it (usually depends on how bad it sets with me). So far I enjoy the story even if I don't agree with the options/choices all the time. (looking at you vampire choice -.-)
And its the "dark path", not the "evil path" so i think its fitting, killing your enemys always is definitly darker even when its justice or reasonable.
There doesnt seem to be a simple Good/Evil lore in Nephilim which is potrayed with angels being very cruel for example or with a friendly vampire-goddess. We will just have to wait and see to know more about the lore