Hmmm... could you just make it so that the gunner is kinda belted into place and that when the unit is 1/2 damaged it can no longer attack? I mean, if hes belted in you cant really tell if hes dead or not so you dont have to have a seperate animation. If you damage the jug enough, and you hear a dwarf inside go "goodbye cruel world" and BOOM it explodes, this may not be as cool but it would work.
OR you could have some kind of dwarved guard tower instead that doesnt move and therefore doesnt need a cockpit.