I agree with your answer for the most part, but it's basically the status quo anyway. Some questions were just mistagged, and I've retagged the john and apostle-john questions to john-apostle, since he's the one they were about. I've also submitted a tag wiki to make matthew's scope explicit.
Here's where I have minor disagreements with your answer:
john should be blacklisted, since it's ambiguous: questions should use john-apostle for the gospel writer, or john-the-baptist for the other major John.
For the most part, the convention is that the Bible book "Foo" will be tagged as
foo, and sometimes given synonyms
book-of-foo. So jude fits the convention. The only tags about books of the Bible that don't fit that convention are book-of-james (3 questions) and book-of-judges (6 questions) and the four gospels. I don't think those exceptions are worth our time to "fix" either, but if you want to fix the James and Judges questions, have at it.