I, too, had this issue today and came here to find out what the problem was. I also had one Risen trapped underneath the docks.
My conclusion was to go as close to the area where he was as possible- Trahearne (the NPC) would follow wherever I was going. Then, I would summon either my Sylvan Hound/Elemental and it would detect that the Risen was there and try to go after it. Trahearne would also then start attacking. Somehow, Trahearne was able to go through the docks and fight the Risen (if that makes sense). The Risen was then drawn out to the point where he was half in the docks/half in the water and I was able to go underwater and finally kill him. Took me a while to figure this out, and I know this is kind of not a clear explanation, but you can give this a try- just try to make an NPC detect the Risen and magically walk through walls to kill it.