Hi there, long time Lurker first time poster! (Hate saying that, but eh, best you all know).
I have the same problem, with the reputation "quests" diasppearing from Mr. Helper.
I want to get 75 rep. with all major factions. With the Rebels, as ever, I played through the quests...and when I got to the desert, I decided to help the Nomads (again), but I wanted to get in to Ishtar without a sword in my hand, so I decided to use Mr.Helper, and thought to edit my rep with the orcs later...but once I left chat with Mr. Helper, the option disappeared. I went back to the .ini file and turned the cheats off, saved in a new file, then turned the cheats back on, but still there're no reputation options with Mr.Helper...
SO! Are there any other ways of editing my reputation with orcs? I want to eventually kill them all and liberate Mytana in the name of the Rebels (yes, again). Also, I'd be happy to accept any advice to steer me away from the path of the rebels/rangers/nomads, as everytime I play through G3, I always help them, even when I promise to help the Orcs and Hashishin!
Sorry for the looooong first post, any help with editing my orc rep. will be greatly appreciated, thanks.