I think that anyone who's played planetarion for any length of time can relate to making mistakes - pulling an attack fleet through on roids... recalling a fleet defending a HC instead of a probe fleet... whatever.
I'd actually like to see Missions modified more than some tick box.
An idea INSTEAD of the tick box (won't be popular with defence-orentiated people):
you can modify some sort of continue/recall box on each fleet. When the tick comes, it either ticks onwards to it's target, or back towards home.
It'd reduce accidental mistakes, except in things like speed games and those last minute fleet pulling things, but it would cut down on accidentally pulling somewhere in the tick, as you could just reset the fleet back to attack (some drop down box or toggle option or something) and change the relevant fleet to recall.
I also think that either there should only be one "launch" button on the missions screen, or that the launch button launches all fleets with co-ords entered etc, but that's different
(one launch button would mean having to move the mouse instead of just tabbing etc)