It'll matter to the minions of the Order, though. (I guess Bak might replace Komui, unless they decide that Bak's opinions are too similar to Komui's and they want someone more loyal. Komui is also the only thing preventing Allen's immediate arrest.)If he dies along with HQ, of course everything will change - the whole war will take a totally different course.
If he is the only one to die - Order will probably not change it's structure. He will simply be replaced with someone else.