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Theological Implications and "Scientificness"

It is popularly believed that if a theory has theological implications, then the theory is somehow "unscientific." A post at the Florida Student Philosophy Blog challenges this claim. I think the article is unnecessarily long and involved, but I'm quite impressed with the insight. The argument is a reductio that works more or less like this:

• The Standard Model of Particle Physics (S) is a scientific theory.
• Either God exists in some possible world W (P1), or God does not exist in any possible world (P2).
• But all modal statements are logically necessary.
• :. Either necessarily-(P1) or necessarily-(P2).
• But if a proposition is logically necessary, then every proposition entails it.
• :. Either (S) entails (P1) or (S) entails (P2).
• But (P1) and (P2) are theological statements.
• :. (S) is not a scientific theory. (Contradiction.)

That's rather a beautiful proof, isn't it? Of course, the proponent of the strict separation of science and theology is free to respond by further refining his notion of 'implication' to mean something narrower than logical implication, but I've never heard any such account.