The goal of invariant sections, ever since the 80s when we first made the GNU Manifesto an invariant section in the Emacs Manual, was to make sure they could not be removed. Specifically, to make sure that distributors of Emacs that also distribute non-free software could not remove the statements of our philosophy, which they might think of doing because those statements criticize their actions.
Changing the GFDL to permit removal of these sections would defeat the purpose. Nowadays we have to struggle constantly against the tendency to bury the free software movement and pretend that we advocate "open source". So I don't think we can conclude that such precautions are no longer necessary.
