I could see this happening potentially. Apple is continually coming out with new devices, and although the older devices are still popular, there comes a time when you just have to pull the plug.
Although the iPad does have a more advanced processor, much of the processing is dedicated to rendering images for the larger display- so even though the older processors will be able to keep up with iOS6 on the 3GS' small screen, the slightly newer (A4) processors would not be able to handle the new OS on the larger screen, hence the lack of support for that original iPad.
It was a bit more clear they were dropping the Touch 3G and iPad 1, but you have a good point about it still being available on the 3Gs. I feel the reason for iOS 6 still being available for the 3Gs is that not too long ago there were tons of commercials from Apple trying to still sell the 3Gs (for $50?) with a two year contract, so not giving the 3Gs iOS 6 wouldn't be that great of an idea for Apple's customers.