In my opinion in this case we have to make an evaluation of two extreme scenario's:
First scenario, a good player uses the flee mechanic to deliberately "snipe" out an combatant at a time, and uses the flee option to prevent any harm done to his or her party.
Little abusive.
Second scenario, a poor player is losing horribly, remembers that they can flee, flee isn't obstructed, and gets the hell out of that nasty position, they've gained some information, and perhaps even killed an enemy, but they weren't going to win it, and rather than die and reload, they fled.
Desired use of the flee button.
This is important simply because if you change the game for the top end abuser, you will also, change the game for the people who do use the mechanic in its intended use, is it fair to penalise the bad player arbitrarily, just because a few good players will "abuse" the mechanic?
In my opinion the "cure" is worse than the "disease" in this case, the inconvenience caused too all the players who just punched a little above their pay grade and don't want to die (reload) doesn't make up for the very minor abuse caused at top end.
From personal experience I can also just bluntly say that I played the first game at top difficulty and not a single flee was used, I just reloaded, re positioned and face slammed the content till I figured out how to beat it. So I really see no reason as to why the flee option should be nerved for people who do not want to use that method.