I think their proceeding with dunking Sayid when the water wasn’t clear was a mistake. They only did it because they were going to get in trouble with Jacob if they didn’t,and however “alive” he may be now, there’s undoubtedly something wrong with him. Does he occupy some space between life and death, between the timelines,or something else entirely? Also, I seem to recall the water was a similarly crappy color when Ben was summoning Smoky through that cesspool/grated thing a while back…