So I completed the main quest a while ago on my character. Recently, I killed the Nord guy who has the Bloodworm helm on him. For some reason, that character is listed as an essential character, despite (according to what I read on UESP) him not being in any way tied to the main quest. I kill him and take the helm anyway, figuring, "well, I finished the MQ anyway, it should be fine."

Later on, I head back to Tel Fyr to try my hand at plundering the Corprusarium, which I hadn't done when I was there earlier. On a whim I explore the upper levels and talk to Divyath Fyr, at which point he tells me he was disappointed to hear that I didn't fulfill the prophecies, and to go talk to someone in Vivec City (it's the entry B8_BackDoor3 on http://www.uesp.net/wiki/Morrowind:Hortator_and_Nerevarine). It even cluttered up my journal with an entry stating this. Since I already completed the MQ, this makes zero sense, but I figured it probably happened because I killed the Bloodworm helm guy.

Anyway, I reloaded from my last save to get rid of the offending journal entry, and simply didn't talk to him this time, but from what I see on that page there are other NPCs that could be putting these sorts of entries into my journal...

My question is: does there happen to be some way of turning off the "You wrecked the main quest" setting, just so I don't have certain NPCs thinking I'm not the Nerevarine and putting contradictory entries into my journal when I talk to them?

It is a way of reminding you to complete the main quest when you reach level 20 and have a reputation of 50 or more and completed the Cavern of the Incarnate quest. Unfortunately it still occurs even when you have completed the main quest. The NPCs who will remind you are – Crassius Curio, Divayth Fyr, Athyn Sarethi, Mehra Milo, Gilvas Barelo and Nibani Maesa.

Is there a mod that fixes this?

It's possible that the Unofficial Patch might, or another similar mod like that. This bug literally doesn't hurt anything though, it's a minor annoyance the one time you talk to them.