It was the same with Carth. Too whiny many said. Of course if you played a female, Bastila was a cold fish to have to carry along for the ride, playing a male character she was fun to tease.
As to Disciple;
Perhaps the dislike comes from him portrayed as a straight goody-two shoes character and many play DS. Or even when some are playing grey/LS characters, his path/way of thinking is too light side?
I thought Disciple was a decent character all in all, perhaps a little too righteous for my taste if anything but better than Atton for a romance option. (Sorry ladies I thought Atton was ok but he was no Carth or Han Solo). Bao Dur and Candyman should have been romance options...sigh