The filesystem interface is only privilaged interface because it is the kernel knows about. E.g. you can already use FUSE and NFS to roll your own FS implementations, but those do not a microkernel make, because the OS is still in the way dictating the implementation.

The safest way to put the FS on a level-playing field with other interfaces is to make the kernel not know about, just as it doesn't know about, say, SQL.