I don't feel that it's right to call us a tool to them. If you want to say that anyone was a tool, it would more likely be the minor Scions hanging out in the storage room who get sent out on little missions. We are included among the major Scions, directly aided by them, and entrusted with some pretty important missions. They're not asking you to do anything without them, they're asking you to work with them, and since you're the one with both the Echo and the fighting abilities, your abilities are used in the best way by having you fight the Primals while the other Scions do what they excel at (other than normal combat) and gather information for you. Either way, we are never sent off on our own without any support.
Keep in mind that no matter how conflicted we felt about Thancred's possession by Lahabrea (which of course Lahabrea used to twist the knife in the wound), we still would have been forced to kill him if we hadn't been able to save him. And no matter how one as the player might have felt about him, he was still a friend and comrade to their character, especially if they started in Ul'dah. You could say though that the primary reason for saving him was because Minfilia begged us to.
FFXIV's Lifestream is implied to work in much the same way as FFVII's, right? If so, we do know that strong souls keep their personalities and can freely navigate the Lifestream, such as Aerith and even Sephiroth (maybe even Zack to some extent), and other souls are merely part of the Lifestream, integrated into it, until they can be reborn. Since the Lifestream is the lifeblood of the planet in both series, it would make sense that rather than a meaningless heaven, it is instead a way for life to never truly end.