Is it possible for Great People to become automated? If so, how do you turn it off?

If it's a glitch, it has never been documented and we would need it documented.

I started up a game and built some wonders. I made a save the turn before my first great person, and played around with settings.

Even with all three related options checked (units auto-promote, workers start automated, and missionaries and executives start automated), I could not get a great person to spawn automated.

Furthermore, when the great person unit is selected, there is no "automate" option.

In conclusion, either your girlfriend clicked a button she didn't know she clicked, or there's some deep glitch.

Have her start a game on easy mode just to build a wonder (Arabians start with mysticism), and see what happens. Maybe send her a save-game, or have her reinstall. I'm having a tough time rationalizing that she has some weird hardware issue that civ4 is suddenly obsolete.