The only way I can think of would be to put a custom tile down for each settlement and place the besieger's earthwork elements there. The only trouble would be that the earthworks would always be there. In a sense that wouldn't be a problem as pretty much the only time you see a city is when it's besieged, but you couldn't vary the earthworks by faction at all.

eadingas was having some luck with placing a dynamic city on top of a custom tile.

The ideal way would be to tie your 'under siege' model to appear on the battle map (in a similar way to wonders/ships/settlements etc.) but I wouldn't have a clue how to do that.