11 years after the bug was filed, Mozilla has finally started taking action on https://bugzilla.mozilla.org/show_bug.cgi?id=380637, which directly addresses this issue.
In current versions of Firefox (I'm using v.59) there is a new per-site preference, but unfortunately it's problematic (as discussed in recent comments on the bug ticket): It prevents the Backspace and Del keys from working in the browser itself (e.g. to edit entered text), which is likely to be a deal-breaker for most people.
But you can experiment with the current implementation (and hopefully, access a fixed version in Firefox 60) by clicking the
(i) icon in the Location Bar (or by pressing Ctrl-I, presuming you're on a site that hasn't hijacked that shortcut), going to the
Permissions tab, and adjusting the Override Keyboard Shortcuts` setting:
But with irresponsible applications (I'm looking at you, Atlassian) taking over your keyboard without asking, I still find this useful. I'd rather be able to use e.g. my PageUp/PageDown and cursor keys to navigate JIRA just as if it were a well-behaved, user-friendly application. It's a bit maddening but not too hard to briefly unblock shortcuts for the site when I need to write/edit a comment.