Almost certainly not a mistake. But definitely an odd circumstance.
You’re right that generally every airport tries to operate into the wind, and also avoids swapping directions willy nilly. When a wind shift is expected to occur, or does occur, there is often quite a dance to “turn the airport around”. In some metro areas with multiple major airports they all need to reconfigure in sync, so it’s quite a ballet for ATC.
SNA being as short a runway as it is, the airliner traffic really can’t stand to have any tailwind. In the complete absence of wind they could go either way, but IIRC there’s a small terrain clearance value to going south towards the ocean.
OTOH, the mandatory noise abatement procedures to the south are far more restrictive than those to the north. And the southbound procedure requires climb gradients that can be hard to meet if heavy or if some mechanical problem adds some extra limitations.
I’m going to bet the answer is that for whatever reason that airplane (of whatever type) could not comply with the noise abatement procedures required over the Back Bay. Which forced them to go the other way. They may well have had to sit there for 30 or 45 minutes until a small gap in arrivals could be created to let them launch opposite direction to the prevailing traffic.
This is actually a fairly common scenario in Las Vegas at McCarran / Harry Reid. The prevailing wind and operation lands and launches to the west. Into the face of rising terrain, then a set of ridges, and needing an immediate turn to avoid hitting tall mountains. Conversely, going east is over nearly flat terrain, but downwind.
You often a see a jet sitting at the “wrong” end of the Las Vegas runways for half an hour until they can launch the wrong way because they’re just too heavy to go the other way. Back in the days of the 727 this was exceedingly common. As badly as it climbed on all three engines, it really didn’t climb on two. And all airliner (and bizjet) takeoffs are predicated on the assumption of an engine failure on the runway. If the calcs show you couldn’t clear terrain after that failure, you simply don’t go that way.
It would be interesting to know what sort of airplane it was: single prop, light prop twin, bizjet, RJ, or full-sized airliner.