Given this it appears the Talosians were manipulating pretty much everything.
Then why would Spock have gone to the trouble of using the voice synthesizer to fake Kirk's orders?
I don't see the Talosians as evil so much as desperate. At the end of "The Cage," Pike suggests working together, but the Keeper declines, asserting that humanity would learn the same powers and destroy itself, too.
The reason for leaving Pike with the Talosians in "The Menagerie" becomes clear when one sees how the Talosians gave Vina her illusion of health and comfort.
But what about the race of slaves angle? Pike fought that battle and won -- the Talosians considered humanity too wild and intractable. (On top of that, Pike may have been "damaged" in that regard from his exposure to the delta rays.)