Interesting! That could be a more elegant solution. Main problem is, my whole point is to set that flag during the mission via SEXP (it's a wing that warps out, then warps in again... of course the second wing is actually a separate wing, but the point is the "destroyed" status is determined in-mission, when you blow them up

)
Tested "Destroy before mission" on an individual ship in a wing, and it does work as you say, even if the wing warps in later.
But as far as I can tell (and maybe I'm wrong, since there are a zillion SEXPs now) there's no way to alter the "Destroy before mission" value during the mission. Understandable, since in the general case (the ship is already present) I'd expect it to do nothing, and if the ship is not already present then you can put whatever logic you want in the arrival cue instead of using weird dark magic.
Hmmm... might be able to set it via script
