I disagree. The story of Pinterest using Skimlinks became controversial because bloggers made it so. It was fake, manufactured outrage. If they disclosed it beforehand the same thing would have happened anyway. It would've been in their TOS or something and we all know that when bloggers have nothing to write about they peruse a bunch of TOS agreements looking for some outrage to manufacture. They would have come across it, manufactured the outrage, and Pinterest probably still would've ended up ceasing use of Skimlinks.
I'm being speculative here, I know but I think you are too. I think there'd be controversy regardless of disclosure though not disclosing it sure helped make the outrage easier to sell.