Maybe make the military a partial "bandaid" solution? Like you can keep the clowns at bay, but never really finish them off with *just* steel and force of arms.
Considering the many directions this thread has been going in, does it seem to anyone else that maybe the Philosopher Noble should get involved somehow? Like you've got this mysterious little old wisedwarf that just putters around your Fortress, seemingly doing nothing, but then one day, at your darkest hour of need, he reveals himself, and you have to make a choice between listening to the advise of this dusty old nobody you've been supporting for years, and the direct orders of your King.
Maybe the clowns can possess rock itself, and maybe such possessed rock could then spawn critters, cause bad effects (staring, moods, etc.), or even transform into an image of the clown that possessed it (which would then function independently of the possessor, until you slay the clown possessing it--which would allow them to slowly "mine" their way out to the surface, with each mined out square yielding a clown homonculus) until you engrave the evil stone, rendering it harmless, so you have to protect your craftsdwarfs while they go down there and fix the evil leaky pipe.
Engraving as a solution would seem to offer an easily understood, readily available remedy, while at the same time giving the task itself considerably more import.
By the time HFS is breached, how many people *don't* have a small to large team of highly skilled engravers running around, anyway? This might be a nifty way of giving them a little respect.
This also helps assure that you won't lose the body of your Fortress, either, since it's reasonable that late in the game most surfaces will have been atleast smoothed.
Perhaps smoothing the stone by itself would be enough to prevent this sort of clown "infection", with the extra step of engraving only necessary to render possessed stone inert.