Speaking as a former Orthodox Jew, the idea of someone desecrating a Torah scroll fills with me with deep emotional pain even though I know that there's nothing at all holy or sacred about it. Once that sort of offense becomes ingrained it is very hard to remove even when one understands that it isn't based on any actual part of reality.

I don't think this offense is without any basis in reality. If someone goes around desecrating Torahs, you would be completely rational to conclude that he probably has an issue with Jews in general and feel threatened. Even if you no longer believe in Judaism, and even if you no longer identify as a Jew, this doesn't mean that Jew-haters will leave you off the hook. You may disown your religious, ethnic, or tribal affiliations, but this doesn't mean others will stop perceiving and treating you as still bound by them. (As many found out the hard way in Germany in the 1930s, to give only the most dramatic example.)

To get back to the question from the original post, this also implies that it may be rational for Muslims to sense hostility and feel threatened by people who go around committing blasphemy according to their norms, and similar for every other religion. However, it still doesn't mean that every feeling of offense is a legitimate response to hostility -- as with any human interaction where interests clash, we see a complicated interplay of signaling, Schellingian strategy, and dancing around focal points looking for ways to move them in a favorable direction. Of course, things also depend on the more explicit relations of power, wealth, status, alliances, etc. between the parties involved.

The error of the original post is to assume that these complex and highly situation-dependent questions can be analyzed with a naive consequentialist approach, but it would also be an error to simply reverse its conclusion. In different situations when offense is felt and expressed, many different scenarios may be taking place.