Well, apparently Disney does use facial-recognition software via their photographers (it probably is part of their cameras, which are high-end DSLRs, most of which have such technology):
"You may even find more photos than you knew were being taken, as the ship's photographers also take candid photos, which are automatically matched to the appropriate accounts using facial-recognition software." --
http://travel.usatoday.com/alliance/destinations/mouseplanet/post/2011/03/Disneys-Dream-y-New-Technology-at-Sea/145385/1But they certainly aren't being secretive about it; they just don't advertise exactly how they do it unless they're asked (like they obviously were with the above-mentioned article). With their "Memories, Magic, & You" show, they probably started using the software in the parks (at least Magic Kingdom) so they could put together the nightly projected photo show and not get repeats of people so that as many visitors as possible can be in the show.
Anyway, this guy's case probably has to do with his girlfriend getting pics with the characters. The Photopass photographers take SEVERAL candid photos while you are meeting the character, so they probably saw that this guy was with his girlfriend and managed to capture him on a couple pics associated with her. The computers then would have recognized him and given him any photos that had him in them.
I personally have no problem with this. Having been to Disney World this January and last, I think it's great that they try their best to make sure you get every single picture they've taken of you so you can have ALL the memories, even ones you didn't know were happening! And the "Magic, Memories, & You" show is AMAZING, and I wish we could have seen ourselves projected up on the castle, but it's possible we were there and just weren't at a good angle to see (plus, the pictures go so fast sometimes that they can fit thousands of different pics into a single show... and they do this EVERY night with pics that were taken during that particular day; it's so cool and a great way to reminisce about the awesome day you've had!).
Of course, I've grown up around technology my whole life, with a father who worked for Lockheed and is over two decades into a career with Sun (now Oracle). So I've always been a techie and new technology fascinates me, and I love it when it is used to make a person's day better.
No, tech like this would never fly at SDC, but only because it's such a small entity. Disney is GINORMOUS, and with their Photopass and Fastpass systems and multi-day ticketing, it doesn't surprise me nor infuriate me that they use technology like facial recognition and fingerprint ID'ing to make your trip the most user-friendly and memorable trip you can have at Disney.
EDIT: Oh, and this can be very good for security as well (though I don't know if they use it for that), because if someone does something bad, it is easier to find them in the systems. But the computers purge your pictures after 30 days, and I'm sure the same goes for any other info they glean for security purposes. With Disney being so big, security is a huge concern and they want to keep their customers safe.