Make .onion websites open with tor, even if it starts with http://
Solution 1:
I think Dan is actually right on the mark. Privoxy can be configured to pass particular URLs through a proxy but not others. This actually makes it quite easy to have it pass .onion traffic through tor but not other traffic.
You should be able to simply edit your privoxy configuration (/etc/privoxy/config on ArchLinux) and add the following line to it:
forward-socks4a .onion localhost:<your Tor port here> .
For more information on configuring privoxy, see the ArchWiki and the privoxy homepage (linked above).