I think you've undermined your own argument there. All the GNU programs included in Linux are "just applications" too, and all of them can be replaced. (On embedded systems, they usually are, for instance.)
Well, maybe the boundary between an application and a part of an operating system is not clear, but at least the GNU project has the ambition of being an OS, since it compares itself to UNIX.
Also, there is no program included in linux. Linux is a program.