Well, this law doesn't say anything against disrupting criminal behaviour such as a nazi gathering.

It's not a particularly good law, because it is unclear what behaviour is meant. This depends very much on the zeitgeist then. The fact that this law is rarely used is not necessarily a bad sign: it's possible that the law just catches the consensus so well that few people violate it anyway. Ideally the effect of a law should be that people know and respect the rules, not that breaking the rules is punished. Mind, we are not in France here, this stuff is fairly uncontroversial in Germany. I think these attitudes concerning religion belong to the topics where different European countries differ most from each other.

"I wonder what was so different about the Cologne case that made the prosecutor choose to prosecute based on ideological privilege?"

Different from what?