Not everything that the sage passed on came from the Juubi. He had the Rinnegan before he confronted the Juubi. So dojutsus like the Sharingan (which is a step to obtaining the Rinnegan) can be tied back to the Sage himself. Chakra manipulation also came before the Juubi, as the Sage had to use chakra to create the seals used to contain the Juubi. There are at least two things that haven't been attributed to the Juubi, so your argument of "everything the sage passed on was from the Juubi" is false.
I agree with Kael03, so this seemingly mindless destructive creature made the rivers, trees and forests, etc. All humans have chakra, the sage with his rinnegan(mutation or otherwise) divined(figured out) what you can do with it, taught how to hone and nurture(increase) it and such.
I believe the sage and least had the rinnegan, because how in the world would a normal run of the mill human figure out a way to contain the juubi inside himself. Naruto in a pure rage state healed fast, and even in his 'normal' state, so I think the juubi and sage shared traits, this is why the juubi has the rinnegan and vice versa.