It does indeed protect from SWJ. Any ability that removes cards from your deck, be they put in play (like SWJ for Souls or Woman At the Well), discarded (like Given Over to Egypt or Gibeonite Curse), or set aside (like SWJ for non-Souls), if used by an opponent, is protected against. Now, the reveal still happens, since the cards are not being removed, just looked at. So, if you used this card against someone who had JT up, you would reveal the top 3 (or 9) of the deck and then put them back on top in the same order.
