I am not sure if this idea has been suggested before, but I reckon that we can draw some inspiration from games like Puzzle Pirates for how sieges might look like. In Puzzle Pirates, when one desires to blockade (siege) an island, a time is set up for when the battle will take place. The prearranged time for the battle ensures an intense event where all of the vested parties turn up to do battle.
How I envision this might look like is this:
1) The party that desires to conduct a siege should be able to declare an intent to siege by interacting with the said plot in some say, e.g planting a siege flag on or near the plot. The defenders of the plot then have a window (maybe 1-2 weeks) of time to declare when they are going to defend, which has to be at least 24 hours notice. The battle will commence at the time declared by the defenders. While the village in question has a siege flag on it, their charter stone is disabled. Indeed, the defenders may attempt to sneak out valuables in that time but that is a reflection of the reality of sieges-sometimes, when trying to break into a castle, whatever thing you are looking for in the castle may decide to sneak past while you are trying to break in.
2) The siege flag gives the attacking party a plot of land of some size in which they can construct a camp of some sort with siege engines etc. The camp will not be able to be vandalized until the time of the battle. Likewise, siege engines built on that plot will be unusable until the time of the battle.
3) With the battle time having been declared and the siege engines built, all the two parties involved has to do is turn up at the time of the battle. The attackers win by breaking into the village. The defenders win by either destroying the siege flag or successfully preventing the attackers from breaking into the village after some hours of defending, when the siege flag will automatically expire (simulating the attackers running out of resources after a lengthy siege as in rl). During the battle, the siege engines will be vulnerable.
After the siege, the village should be immune to more flag being placed onto it for a certain time (to prevent spam). The siege flags should also have some sort of significant resource cost.