If you can't avoid the enemy engaging you in combat in the first place, then apparently your scout isn't quite fast enough to escape before it's destroyed, or its sensors aren't good enough to avoid stumbling into weapon range or being ambushed. Them's the breaks.

You can check out the stats of enemy fleets to see how fast they're able to go and that sort of thing. So long as you stay vigilant there's no reason for a fast ship to end up in a fight it can't win.

It wouldnt be tactical combat, when attacked a dialouge could come up, saying "fight or retreat" if your ship has no movemnt points left, it has no choice but to fight.

Consider those attacks on your lesser ships a form of ambush.