Quote the Bible as you do any other book. Yes, it has strong religious ties, but, nothing bans Atheists (or anyone else, for that matter) from purchasing the Bible to read. Topitmunkeydog, if you'd even like to quote the Bible in your film, (as with what you've said about it, it may fit) then, I'm fine with that. If I don't like the film (especially if it offends me) I'll just not rate it, and never watch it again... It won't harm you, and yet, no one really "cares" in the end...
The only thing you should be worried about is if your video starts a "religious war" on the comments. Even then, on Youtube, you can just delete comments.