It appears we missed one important rule last time we played, which would probably have changed the game quite a lot: terrorist units must be at least as large as the development they are attacking (http://www.forumsvibe.com/thewaronterror/viewtopic.php?t=204&mforum=thewaronterror). This would have made, for example, attacks on cities deep in "friendly" territory much less likely - or at least, much more expensive for the empire funding the attack.

(I don't think we missed any of the other rules from that list.)