Having a large stack of troops on their land does seem to improve your chances of getting a deal out of them. I would suggest maybe hanging around for a couple of turns in a defensible position to increase unrest and hurt their bank balance.

The thing that annoys me tho is the fact that if you attack a fleet blockading you (or a beseiging army), your relations with that faction decrease .... surely this is not right as you are just defending your lands etc.

Although you can attack these armies/fleets and not be excommunicated if threatened by the Pope.