Many missions require the heroes to be in the evacuation area to win the mission, and in those missions, instead of retreating, a defeated hero remains but receives only one action per activation, which they can only use to perform a move action...

So, dumb question, but... what if that hero is stunned? rules as written, it takes a special action to remove the stun, but the only action that's allowed is move (so the defeated hero can't remove the stun), which is not allowed when stunned... does it mean this is game over for the rebels, since that hero now can't make it to the evac zone?

The heroes become incapacitated, and incapacitated heroes cannot have conditions.

Yup. See Incapacitated from the Rules Reference Guide.

aah! thanks!

No matter how much I play this game, there are always forgotten rules that seem to pop out of nowhere!