So... you would have to scout every city in the opposing alliances to figure out which two towns. If every town sets a ward against scouts you lose at least 400 scouts per city times maybe a thousand cities. Not to mention any losses their defending scouts may inflict. Sounds expensive.
Once the correct cities are discovered and you have a target, then you can send assassins. Meanwhile the target city resets its runes to kill 400 assassins and their whole alliance piles defensive diplos in as reinforcements, so you end up sacrificing many hundreds if not thousands of assassins trying to kill one commander, who may get lucky enough with defy death or whichever talent it is to survive a few waves of assassins who make it through the defense. Also very expensive.
Is the target commander required to remain in that city with his army, or can he hide out in the countryside? If he can hide then not only will you be dealing with the runes and defenders once, but possibly multiple times trying to catch him at home. Very, very expensive.
Then assuming you eventually succeed, only then are you allowed to send a siege, which an entire alliance will be focused on breaking?
If I'm reading this right it sounds mainly like an operation which is guaranteed to cost many thousands of spies, many thousands of assassins, and probably hundreds of thousands of troops. There had better be one heck of a price payout at the end.