I'm in almost the exact same boat you are right now -- Apache 1.3 (just-died Red Hat) to Apache 2.2 (brand-new Debian). [webmasterworld.com...] Thank you for posting your question because we were exposed in the exact same way. YIKES!
My husband figured out two ways to the same end: hiding /home on the machine's IP.
1.) Go to /etc/apache2/sites-enabled and remove the (symlinked) "000-default" (This leaves "default" in sites-available untouched.)
- OR -
2.) Login via command line as root and use the "a2dissite" utility. https://help.ubuntu.com/8.04/serverguide/C/httpd.html
He used the latter and now a direct call to the machine's IP results in the generic 404 Not Found. Attempting several IP/knowndir destinations also yielded 404s.
I truly hope you're having more success overall than we are. We've been at this for days and still every hour brings with it a new error we've never seen, a new config we never had, another snafu we've no clue how to fix, another thread with more questions than answers. Good luck!