I don't particulary like the idea myself. It would feel too much like altering the rules as you play. If you play for the sense of immersion it may be worthwhile but the potential for exploit (if only through micromanaging) worries me. To each his own I guess. (Note if you allow the setting before game starts only then I would be more willing to accept the idea)
Since you're making the suggestion for a mod, I'd like to see how it works if it ever does.
Here's a suggestion. How about you let civs at war have two turns of moving units? For example, in a game with 3 civs: A, B and C.
A and B are at war. C is neutral. Turn order:
A has his turn.
B has his turn.
C has his turn.
A has an extra unit-movement-only turn.
B has an extra unit-movement-only turn.
Next turn etc.
You would have to sort out lots of minor details like not allowing units to heal in the same turn, and make it only units inside enemy or own borders who get the extra move (to prevent faster explorers just because at war) etc., but perhaps this can be thought through by someone more keen? Obviously also exclude settlers, workers and generally most non-military units from the extra turn.
