Modern Terrorist: I'd make it a tactical nuke, 1-2 bombard range, very high cost, invisible, 1.1.1, and give the unit the poison gas animation for it's bombard attack. This way you get a lot of resentment for using terrorists, but they're still effective.
Ancient/Middle Age Terrorist: High bombard with bombard effects, 1-2 bombard range, med-high cost, invisible, hidden nationality, 1.1.1-2, cruise missile, and precision bombing. Then make different animations for different eras, and when precision bombing comes you can take out buildings.
Of course, the AI might stock them up a whole bunch and send them in all at once, that would destroy most of your improvments. So these units could get really annoying. This is just the way I'd do it, it may not suit everyone.