That was my interpretation as well... that Jacob saved Sayid's life but couldn't save them both (for some reason?)
Clearly, this was to get Sayid to return to the island. Just like his visit with Hurley. If she is still alive, Sayid stays on the mainland, isn't messing around with Alana, etc. He wanted that group to return to the island so that those characters (Jack, Kate, Sayid, and Hurley) can go back in time and change the past. If those characters aren't there, Daniel's plan dies with him. Jacob is doing this to save himself.