Generally speaking that's true.
It still has nothing to do with religious prejudice but, as stated in the comment, with culture.
The so-called "christian" party that keeps a stronghold on Bavaria for 50+ years can do pretty much whatever they want (including large scale corruption) and still get reelected with a comfortable margin. But they're weaker these days and need a minor partner, and in the other southern state they've been shown the door in March.
Protestants.. well, they protest at some point ;-)
Not saying that there's no corruption in the northern parts of Germany, but either their smarter at hiding their tracks, they're really less corrupt than in the south, or they're dumped more quickly (and thus weigh their benefits by corruption with the risk of losing officed more).
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