No offense, but there was a LOT of infighting and deaths. Members of the Guild were focused on other things.
Plus, once Mercer became Guild Master the issue was swept under the rug because the Guild was in decay. He couldn't have asked for better cover, and he had already scapegoated Karliah and slandered her name, and infighting had put an end to that topic. Mercer avoided suspicion without any effort. Besides, it's reasonable to think that the leader of the Guild wouldn't stab it in the back.