Well, if friendly forces and civvies did their own little thing in the player's turn, I can see some consequences of that.
1) Even though civvies would be programmed to run away from aliens, they would still trigger reaction fire, and friendly forces are likely to be programmed to seek out alien forces, which would trigger reaction fire. A savvy player would sit still and let the ai "do his thing" before taking his own turn, to a) draw reaction fire to allow his own troops to move unmolested and b) prevent stray triggered reaction fire from harming his own troops.
2) The same savvy player would also sit still and wait to prevent his own bullets from intersecting with the body of a fleeing civvie, or advancing friendly force.
In both cases, the player is being made to wait for the ai to do his thing to prevent unfavourable outcomes from occuring. And even if the ai npcs went Benny Hill spastic at the start of the turn, that still wouldn't prevent 1) or 2) from occuring. The solution from my point of view is for Yakkety Sax to start playing the moment the Hidden Movement screen comes up, for all ai npcs to go into TURBO HYPER MODE and get their moves done as quickly as the engine will permit.
EDIT: As an addenum to that, the only ai npcs that I would prefer move at "normal" speed when I see them would be the aliens. It may be a little jarring to see civvies run around like a butterfly on crack, but at least they'd be done quickly.