If the semi-colon is meant to mark a subtitle, but the reasons why God is still great does indeed make up the second half of the book, I'd consider changing it to a single unpunctuated sentence (or use parentheses) so that the notion that this is still a primarily positive book gets relatively equal emphasis.
IMHO, if the latter bit becomes a subtitle, it could get lost as several venues tend to omit subtitles or place them on a secondary line on the product page (such as you might see at Google Books), so your book would appear to be primarily negative to the casual browser, instead, and that doesn't seem to be the effect you want?
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