I like your thinking. It gave me an idea: sieges should be hard, but also more or less fun. Besiege a large city would take months, but during those months you would be able to do something more than just looking at the screen. Missions, infiltrations (the leader of the siege asking some of your best soldiers to infiltrate, and you can choose to lead them or not. Then going into a dungeon with enemy guards, to represent a secret passage, etc) to poison their water supply, to steal their food or to open the gates, the enemy could be able to make small exits for surprise attacks (in the middle of the night, while waiting, you get the message "¡A group of enemies is attacking part of the camp! ¡Defend yourself!", and you would fight with just some of your soldiers (or companions) against some of their troops...
Yup, any of these would make things more interesting (not to mention realistic!). Actually, any action while besieging would be welcome - I hate that you actually have to "leave the siege" to do
anything at all! A siege was rarely just a "tower to the walls" kind of deal - for both sides it was rather about a battle of morale, starvation, alliances and betrayals...
Same thing for when being besieged: all you can do is run away or sally - there is also some talking with the enemy, but there's a lot more to achieve there (for instance, if there are multiple lords attending the siege, you can try to bribe one of them to leave the siege). Also, like you said, mini-sallies would really be very interesting - skirmishes were a great part of some sieges. Night warfare was a great way to demoralize the enemy and it makes me think of one of my favorite war episodes:
http://en.wikipedia.org/wiki/The_Night_Attack...

Maybe (like 20% chance) you could recieve a message from the Guildmaster, saying that he will help you make peace with the leader of the city if you promise not to sack it.
Also, a very much encountered situation in medieval warfare - the Guildmaster or Mayor would lead separate negotiations with the besiegers, usually ended in surrendering the city for a fee and sometimes having a handful of knights disagreeing and locking themselves up in the keep...

Very, very good idea!
Also, you could be able to sack a city or castle if you conquer it by the force of arms. Also if they surrender, earning lots of infamy. Sacking of a city/castle would be quite profitous for you, and would raise the troops morale to the top. You spend a day or two sacking and then it's done. The city is impovireshed, the population does not like you, but you have earned a lot of money and you have lots of food. A sacking always should take honiour from you, but if you conquered the city by the fight, you'll only loose 2 points, let's say. If you sack it after a surrender, you loose 10.
As sacking was part of any successful siege - unless negotiated differently - I don't think you should necessarily lose honor if you sack it after having to fight for it. This was a very normal mechanism back in the old days (even today, look at the modern wars), since the army payment was usually kept to a minimum, while the soldiers were promised booty. No sacking meant no booty, so the morale of the army would go down following such a decision. Like you said, and so you can balance things quite well, if you decide to sack a city/castle, then you lose indeed some honor, lose some popularity with the city, maybe even have something destroyed in the process (see the fires of Constantinople during the 4th Crusade), but your army gets a major bonus morale (as contrary to the tiny morale boost which happens in the vanilla game when conquering a city!); if you don't sack it, then you may actually gain some honor, get an increase in popularity, etc., but the army morale founders... Also, this decision should contribute to having the city/castle attributed to you by the king - maybe a connection can be done between the popularity score and the king's decision...
Cheers,
PKR.