Mission expired with the Pope = reputation drop

I had to stay out of battles with Milan for seven turns or my reputation with the Pope would drop. I just had put my cardinal for a Pope and my reputation was 100%. But after couple of turns Milan blocked my port and was excommunicated. And guess what - I get a message "mission expired because Milan was excommunicated" AND got 3 points reputation drop! As if I failed the mission.
This was without the patch, but the patch info says nothing fixed about the missions.

BTW - now as I think of it I remember when I joined a crusade. At the end of the turn the crusade target was conquered and I got again the message "mission expired" and the sounds of disappointment. And the next message was I receive few florins and little experience for the crusading units; but because there was no time to get the message "Crusade grows" it seems my mission was treated as a failure again.

Maybe the "mission expire" failures are giving less reputation drop then "mission failure", but in both examples actually my mission was successful...