I've always had it ruled (including at Nats 2011, though I don't remember the specific judge) that "putting a Lost Soul in a site" can only be achieved by 1) putting it in an unoccupied site during your Prep Phase per game rule, or 2) using a special ability that lets you put a soul in a site. I've specifically been told that exchanging with a Wanderer already in a site does not trigger these Souls.
Also, exchanging one of the Judges angels into discard pile is NOT considered a discard of that angel, so why is this exchange different?