Will we then find the Winnower/Gardener(if they are the same) and use it to defeat the witness?
The Winnower in my mind is the sole source of Darkness, so could he drain the witness of its power?
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It is unlikely that the Winnower would ever help, at least directly, similar to how the Gardener doesn't help us directly. As for draining the Witness of its power? It may be possible, but it'd have to be us taking it by force, rather than the Winnower itself. If we ever do fight the Witness then that'd be an interesting mechanic to fight him with.