Yes, you are reading me wrong.
However, the Eberron campaign takes place a mere 2 years after the end of a continent-wide war that lasted 102 years. The army numbers I quoted there are probably quite small. The CS book does not go into details about the standing armies (I'm sure the 5 Nations sourcebook to come will mention them).
Scarface, I doubt, tried to take on the US army. Oh, and someone destroyed an entire country in a matter of minutes. But, it was NOT someone who was 20th level, I can assure you. House Cannith was probably experimenting with a doomsday device. This has not been gone over in the setting.
So there are kingdoms out there that still have large standing armies. Not to mention the Warforged, which, if the scenario you point out happened, there would be at least a couple of nations that would put in more orders for Warforged from House Cannith. Their resistances to certain spells would come in handy.
Fact of the matter is, yes, I expect the high level characters to affect the setting. That is the whole point. But they are not going to roll over the continent and take it over by force. If kingdoms worth of soldiers, mages, and clerics couldn't do it in 100 years, I don't care if it's 6 20th level characters, they aren't going to have any easier time of it! I don't see why that is so hard to accept.