Is git-checkout's restoring d/f conflict really sane?

$ echo data > one $ git add one $ rm one $ mkdir one $ echo two > one/two $ echo three > one/three $ git checkout one $ ls -l one -rw-r--r-- 1 pclouds pclouds 5 May 14 16:36 one

Replacing a file is one thing. In this case we're deleting a directory and unknown number of files inside (in this case 'two' and 'three'). Is this really a good thing to do?

If it's not but too late to do anything about git-checkout, could git-restore do something better (and exactly what)?