Originally posted by: Everon
I'm pretty sure that the organization just wants Naruto's Kyuubi. So whether or not Naruto has to be alive is uncertain. They might need to perform some new jutsu that we haven't seen to extract the Kyuubi and then just toss Naruto aside. Or they might need to keep Naruto alive indefinately to use the Kyuubi's chakra.
I think they need to have Naruto to be alive to extract Kyuubi because if Naruto's dies, Kyuubi dies. (in theory) Otherwise, Kyuubi wouldn't give power to Naruto if Naruto being in danger didn't mean that Kyuubi be in danger.