So there is a lot of confusion going with regards to Sayid and his current state. While whittling down the hrs and mins until episode 5 later tonight, here's my idea on what might have happened.
Jacob appeared to Hurley in the night (it was dark) and told him to bring Sayid to the temple, along with the guitar case. What happened next? The losties went back to the Swan pit to try in vain to rescue Juliet.
Sometime later, the sun has risen and it is bright. Hurley and co. decide to head for the temple then, while Sawyer buries Juliet.
I believe that Sayid should have been taken to the temple right away, when he wasn't completely dead. I think what happened was that he died long before the Losites headed for the temple, and we know dead bodies can't be left unburied and exposed on the Island. Why? The darkness claims them.
I belive Sayid was long dead and infected by the time they arrived at the temple. What they should have done right there was burned or buried him, because he was already gone. I think that the spring, despite the murky water, did in fact work, and it borught Sayid back. Problem was, he had been dead for so long, his vessel (body) had been claimed by the darkness.
So in short, the Losties dropped the ball, they didn't save Sayid in time and now they are responsible for whatever he has become. Jacob was counting on the Losties to save Sayid in time, and even mentioned how grave the consequences of his death would be if he died in his note to Dogen. (Shit? Meet Fan.)
I am aware that this theory doesn't touch on the water as a factor in changing Sayid even though we've been told that it is. I really don't have a solid idea on why that is. Hopefully we'll find out later tonight?