You'll note that his main point is that GRAVITATIONAL force is acting equivalently across the rocket. This isn't the case in interplanetary space.
EDIT: okay, that's not as precise or helpful as it could be. Suffice it to say that out at Kerbin's orbit and outside its SOI, gravity is negligible compared to everything else acting on the rocket.
Also, Mr. Manley doesn't really get into the root cause of why pendulum rockets are unstable, which is outlined here (https://web.archive.org/web/20091018232320/http://geocities.com/jim_bowery/pendrock.html) but which basically boils down to the assumption that the rocket motor is going to be fixed relative to the mass that it's dragging, which isn't necessarily the case, since you can free the gimbal on the Klaw.