I have not read the whole post, so if this has been said, I apologise, but I had a brain wave.
If tunnelling went ahead - a few points really.
Firstly, the AI would not realistically start the tunnel two miles away, they would get as close as they could safely and then begin digging. This allows the dwarves to 'sally out' and quickly attack the sappers, before retreating inside. This promotes a more active defence, which I think would make a much more interesting experience. Furthermore, there are a million suggestions for counter tunnels or prepared defences, which seem another valid way to tackle tunnellers. This presumes a working Military, which goes without saying, but that relates to all sieges. The siege would not all be clustered around the tunnel, especially if camps are formed, since attackers would have to eat and sleep, and would not want to draw attention or crowd the sappers. The timing aspect of this adds a tactical element to sallying out.
My main Idea relates to how to deal with the tunnels left behind by tunnellers. Make them collapsible with some kind of mechanism, IE, using the engineer type skills and some basic engineering items - mechanisms and levers. The player 'builds' two spots (at the beginning and end of the tunnel) and then links them to a lever. This level is pulled, the tunnel is collapsed, either all of it, OR just the two ends, but the intervening tunnel is hidden. Thats a minor point, I wouldn't care either way.
This means those who want to completely remove the tunnels afterwards can do so promptly, those who want to keep them, can. It also allows you to perhaps prepare a trap for the next siege, by collapsing the tunnel when it is reoccupied by goblins. Make it usable only on none player constructed tunnels (if thats code-able) to prevent supper easy traps and all other possible uses of the 'collapse' designation or build, and voila.