I'm going to have to go along with the "breaking stuff" theory. GM can't control how you drive a manual, they can with an automatic. What do they call it, torque control or some such? The change probably has to do with the demand for insane (compared to 15 years ago) amounts of power in the rigs...if the motors were as weak now as they were 15 years ago, you couldn't hurt the drivetrain if you tried. Now you've got issues with the 14FF enough that there is an 11.5" diff.
I doubt strength of the transmissions themselves are an issue, from what I understand, the new autos used in trucks are absolutely massive, comparable weight/size manual has to be at least equivalent in strength.
I think dropping the manuals in the trucks was dumb, but of all the people complaining about it, or even solid front axles, how many were actually in a position to BUY a new truck, and thus took their business to Dodge or Ford? Same story with the Camaro: uproar that it was disappearing, but sales sucked.
You are already seeing the resurgence of the manual in American cars, I hope people are realizing that it is indeed more fun to drive a manual than it is an automatic.

With the rising cost of fuel, more and more may go that route, (see the dominance of manual transmissions in Europe and the $7.70/gallon diesel price thread) although the hybrid vehicles apparently remove any possibility for a manual, so remains to be seen how popular those get.