Ok, I fixed this in 0.2.12, but of course, it's still experiencing the networking overhaul. None the less, we should have a bug report for this if there isn't one already and I want to make sure it gets tested, etc.
The way I fixed it is that the attacked unit will flee to 1/4th of the distance between him and his attacker (in the opposite direction), or one space, whichever is greater (in case the guy being attacked is practically blind and 1/4th the distance wont result in any movement). For comparison, when units that cannot attack auto-flee, they flee 2x the distance between them and their attacker. I don't want such serious fleeing because these are units that can probably retaliate, they just can't see their attacker. If they aren't fleeing far enough, we can change it to 1/2.