Remember the French Lady? In the first season, she talked about killing her entire team because they were sick. In the fifth season, the flashbacks showed her team, and they were obviously sick. Not physically sick, but they seemed to have turned evil. Also in the fifth season, Sayid shot Ben, and Kate brought Ben to the others. They said that if they fix him "he will never be the same", implying that this "darkness" is in Ben as well. As usual, we will not totally understand this "darkness" until the end of the show, but I imagine it is like being possessed.
I am sorry to say the user right below me is incorrect, as we never saw the water Ben was put into. The episode entitled "Whatever Happened, Happened" ended with Richard taking Ben into the temple. However, we never acutally saw what happened to Ben inside the temple. The next episode, entitled "Dead is Dead", starts off with Ben inside a tent, and he has already been healed. Therefore, we never saw what the water was like. However, if it were clear, I imagine Richard would not have said "his innocence will be lost" and "he will never be the same".