SMWhat said:
Why don't you switch 'em at an earlier point in time? Let them settle into their new roles, with their different personalities.
Meaning that either Gendo has a backup plan when he doesn't show up, or Rei goes out, loses and 3I happens. And 'Sending Section 2 to fetch Matou' doesn't count as backup plan. They can't find a runaway kid in Tokyo-3 for days - one of their pilots no less - and Shinji is hardly a ninja or invisible. Section 2 might as well be useless.
Either way, it's hardly the hellish situation some of you think it'd be for Matou. Worst case scenario, he dies like everyone else, and it's doubtful whether he'd know it or not.
If you really want to screw Matou up, send him in the Higurashi world. <_<