Here's a proposal (since we know this isn't going to be changed any time soon we might as well aim high): The civilians are stupid and scared, so it makes sense how they would run at the soldiers screaming. But when three of them surround my best sniper and stand there oogling at him, the logic breaks down.
The idea for several meta AIs is a good one:
1. Civvie is clueless, he wanders at a leisurely pace until seeing an alien, a soldier, or a panicked civvie.
2. Civvie panics! He will run away from aliens he can see, though he might run into one without the TUs to turn around. If very close to an alien and with very low TUs he might crouch and make a mess in his pants, if he sees a soldier he will run towards him and bug him for a turn or two, something we all hate, but it is partly realistic.
3. If the civvie can't find help he may seek other civvies, this will actually make it harder for the player, and easier for alien AIs.
4. The civvie (or the small group they may have become) eventually gives up and hides in a corner, preferring 3 wall corners, in smaller rooms, and with fewer doors.
Now, while the civvie is bugging the soldier the soldier could use up TUs to direct the civvie to an area (as I understand the maps are already split into "areas"). Naturally the more complex the directions the more TUs spent. Civvies with weak mind attributes may make mistakes in their extra-stupid panicky state.
To keep things simple, the civvie restarts his stupidity process when he arrives, this means that their actions are not very deterministic, but the frustration factor is removed. They no longer suicide and block you do death, but you still get the feeling you're herding cats. Some may wander back into danger while others will stick around long enough to get to stage 4 and hide in a slightly safer corner.
Well, that's as overcomplex as I can make it =)