I took my level 3 Iksar monk through the East Freeport tunnels to catch the boat. To my surprise, Harkin, Beur, Elisi, Gren, and Veronica were all dubious to me. If your faction is clean, these guys probably won't come after you.
This guy is in the tunnels, secret entrance through Seafarers or swim past shark through stone wall. Follow prompts. Simple quest takes you to Theatre of tranquillity in West Freeport, do this with Nestral T'Gaza quest of the same nature. When you return to Harkin you get positive faction with Freeport Militia and others, and no negative faction hits.