I agree with TRIFORCE89 that "Book of Mudora" seems to be the most appropriate translation. Not becuz of the "Book of Magic" or anything (since that is actually "Bible" in the original Japanese version), but becuz it lines up with the various books that make up the Tanakh and Bible. So long as you UNHIDE the religious references surrounding the book and its use, I think it will be possible for players to understand the reference, unlike the NoA translation. Plus, unlike "Book of Magic", "Book of Mudora" is a translation from the developers.
I strongly prefer Agahnim to be "a wizard disguised as a priest in order to trick the King". He's clearly got wizardly powers, so there's no tricking the King involved in him saying he's a wizard, but the point is that he lied in order to get close to the King. Right? I'm not misremembering? A priest is obviously safe, but a wizard not so much. Since A Link Between Worlds takes place after the events in A Link to the Past, the truth that Agahnim is actually a wizard would be out, so it actually WOULD make sense for him to be called that instead of "priest" in ALBW.