Without javascript the remote page should simply ignore rel="facebox"
and behave as any other link to an external page i.e. open it in the
same window.
What behaviour are you seeing?
On a related subject, it's also worth considering that search engines
will ignore the javascript and index the remote page in it's raw
unFaceboxed state. If visitors access the remote page directly from a
Google result will they be provided with navigation to the rest of
your site?