Cease and desist is weird. You can leave armies sieging enemy settlements and the pope doesn't bat an eyelid. What you can't do is actually attack. Settlement has 8 turns to go until sally, get 7 turn desist order, just sit there. Pope is happy, enemy forces are depleted, you sack city with 1 turn to go. Magic.

As for them getting the same mission they may well do. I have seen the Scots/French excommed when they attacked after the order was given to me as the English. Usually happens when they attack a city. So if you're feeling particularly evil, take all but one (peasants or some crap unit) of your forces out of a city and have them hide in the bushes near by. Sometimes the AI just can't help itself.

Edward: Hey, Edinburgh is defended by a bunch of scrawny peasants. Lets to it.
General: But the Pope!
Edward: Screw te' Pope! I want my city back.
*Pope excomms Edward*
*English attack from the forest*
Edward: Doh!