How to reinstall Java 6, for development for Android, on Mountain Lion?
From my understanding the actual components that need to be removed first are in /System/Library/Java/JavaVirtualMachines/*.jdk

So if you get rid of those:

$ sudo rm -rf /System/Library/Java/JavaVirtualMachines/*


Also, as you mentioned, you're supposed to remove this:

$ sudo rm -rf /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin


At this point it should simply be a matter of downloading 1.6 and installing it.  If you do $ whereis java you will see that the java binaries are stored in /usr/bin/{java,javac,etc}.  But $ java -version apparently gets its information from the first folder I mentioned you should delete.

After you remove those, try running $ java -version again.  You should be prompted to install it.

Hope this helps!