To say that APE can cause kernel panics is a sign of technical ignorance. Because APE does not affect anything on a kernel level, it by definition is isolated from causing panics.
My system is stable with multiple APEs installed, including one I've written myself. I know the technology it uses and am quite confident that it can't cause hard lockups or kernel panics, because it only affects desktop applications like the Finder.
My suggestion is that you pay attention to other programs that you install, particularly ones that come in .pkg formats, and use a program like Pacifist to check the contents of suspicious addon .pkgs before installing. Doing this will save you more trouble than uninstalling some mostly harmless APEs will.