well i read that link and this happened before i even met ether of the two in chorrol... is their any other explination??? and on a side note who exactly are the Deep ones?
Possibly a reference to the Dwemer or the Cthulhu of H.P Lovecraft.
I totally read too much.

Heres what I take of your situation, and I think it may be a bug or a crack in the script:
- The quest has not yet been initiated, ie Dar-ma has not been kidnapped. (Though, odds are she has been, since Darma automatically approaches you to say hello when you go to Chorrol in midday. After that, she should get captured.)
-You picked up the strange diary while you were doing what you do best in Hackdirt. This initiated hostile behavior from hackdirt residents. However, you did not continue the quest.
-As happens a lot with NPCs, the residents go after you, slowly. You've been attacked by people who have sought you for possibly quite some time.
I wouldn't worry too much. You should probably try and do that quest if you haven't already, since I encountered no problems from anything unexpected since I completed it. Start by talking to seed-neeus in chorrol's Northern goods and trade.