Most systems will not allow root to use FTP, which is how BBEdit edits remote files, so you're out of luck there.

Besides, even if you could, that wouldn't tell Apache to reload the config, so you'd still have to log into the server to do that.

It's possible that you could upload/edit another file and have a script on the server copy the changes into the active httpd.conf. That's about the only way off-hand I can think of doing it.