I wonder if we couldn't do something using electricity. The rust would have to be less noble than the cast iron it comes from, perhaps using a suitable replacement coolant (something with salt in it for conductivity) and a negative in the water and positive attached to the engine. I'd think that the electrolysys would move the rust along. I doubt you'd need too much time set up this way, use a car battery or something and see how it goes. Once it's done, flush it all out well and replace it with a "proper" coolant that won't deposit scale/allow rust/etc.
As for scale, acetic acid will dissolve that and thinking of which, it was already mentioned here that it dissolves rust as well. Perhaps a gallon or two of white vinegar in a warm/hot engine would be all you'd need to crack up the scale (and any rust).
Again, a thorough flush and replacement with a "proper" coolant and you should be all set.
Robert