Well, unlike most people I think that Sayaka can life to the end of the series. She got a thought line referring to future events (like Madoka did).
Might it be that Homura wants to prevent new Magical Girls being created. She looked rather suprised that Sayaka became a Puella Magi. Whatever methods she has to know so much (about Madoka and her school and Mami's situation) it didn't seem to include the knowledge of Sayaka contract.