As far as Retreat goes, as has been stated, the change of the rule to allow retreat into a region in which you have 0% MC was more than likely to prevent situation in which a force was prevented from retreating into an otherwise empty region simply because that side didn't control it. In reality, I think a commander, weighing the alternatives, would take the lesser of two evils and retreat into the empty, uncontrolled region.
As has also already been stated, there is gamey taste to "retreating through the enemy". This of course will only occur if the defending force is trapped by enemy and/or unpassable territory. This also assumes that a line of battle is always formed perpendicular to the line of march of the attacking force and that therefore the line of retreat must also be perpendicular to the attacking unit's line of march.
Were there only friendly controlled regions "behind" a defender I don't think many players would argue about any line of retreat into any of them. I know that the devs went to great lengths to try to tune the game to have retreat occur in logical direction - towards a depot, friendly fort or town, or I think friendly forces, but I'm not sure on that last one.
To expect retreat to only be in the opposite direction of the strategic move of the advancing force is not realistic. This game is on a strategic level and there is no representation or consideration of how a line of battle within a region might be oriented.
In general military forces positioned themselves between the perceived goal of the attacker and the attacker and therefore a retreat would coincidentally be in the opposite direction of the attack. I can think of one major exception to this and that is the Seven Days Battle. The attacking CS forces sortied out of the Richmond defenses to attack McClellan to the north-east of Richmond. After a week of running battles however, McClellan ending up almost directly south of his original position.
The few theoretical and anecdotal examples of forces "retreating past" an attacking force show to me that the player was throwing all of his eggs into one basket with the assumption that there was only one possible outcome of the battle in question. But holding some reserves to cover these unexpected avenues of retreat would have changed the situations completely with devastating affects on the defender and the expected annihilation of the of the enemy would have been forthcoming.