If you won't pull the freeze plugs, that's going to make it much more difficult, but understand why you don't want to go that route. If you can hang the engine from the bellhousing side, face down, with the water pump off, then a pressure washer, or even using the pressure part of a hose wand would do a bunch to flush out all the loose crap. Aim it through the pump holes and just spray at every angle you can towards the sides of the bores. Using a coat hanger like Rory suggested would really help also. Otherwise, it'll be a losing battle trying to get all the crud out of those small water drain holes.
I wouldn't want to use any type of acid if not tearing the engine down. I doubt it would be friendly to head gaskets, intake gaskets, any aluminum etc.