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Not sure. Leaving the credits off doesn't really mean that much considering they could just look at another episode. They'd only need to start hassling Matt & Trey anyway.

The last lines spoken by Stan in that episode were basically "go ahead, sue me", which can certainly be read as a direct provocation from Matt & Trey to the Scientology people. By replacing all the credits with "Jane Smith" and "John Smith", they're clearly taking all the responsibility themselves.

Of course, the Scientology people would be fantastically stupid to actually sue, since that would only generate more publicity for South Park and get the episode more widely watched. It's brilliant, really.