Okay, let me lead off by saying that I like saving a lot. It is normal practice for me to have do occasional saves in "longer term" slots and quick save all the time. So, at the beginning of the game, when Darus got killed, I immediately quick-saved. After all, at the time, I didn't know whether or not the assassin would come after me next! I walked over to Darus, picked up the arrow, and got the option to accept the assassination quest. Great, let's hunt this guy down, I thought.

I ended up deciding to load from quick save (for the life of me I can't remember why), and moving over to Darus's body again. Lo and behold, I got no quest prompt this time! Reloading again produced the same results. Frustrated, but not wanting to load from my "longer term" slot, I figured that as long as I had the soul piercer arrow, I could potentially still complete the quest.

Now that I've explored all over Port Kuudad, I know that is not the case. I have just now met Zeblin in the sewers, and he had nothing interesting to say to me. It appears that this quest (and now I know, this trainer), are lost to me forever? That's quite a hefty consequence to loading the game. Is there any way to fix this after the fact?

I know there is. You can delete the map file in the savegame or something. You should make a backup of the save folder (Slot 1 being the quicksave), before trying. Sorry I don't know more exactly.