Example craft: https://dl.dropboxusercontent.com/u/8244638/Control%20Test.craft
Action group 1 for the ladders, climb up to the seat, right click and control from the Kerbal.
No pod or gimbaled engine (so the problem is likely that all the torque*Available variables are 0), but it is somewhat controllable with the aerodynamic surfaces. Anything that can be changed in the code to make MechJeb at least try, without having to add a probe core?

Edit : got to deleted this one.

Did not realize there would be enough information available about control surfaces for that detailed of a fix to work, I was expecting something much hackier! I'll give your build a try at some point.

Yeah I realize that staging-away-root behavior is annoying, it wasn't a serious craft anyway more just a test. Next time I make something similar I'll build top down instead of bottom up.