I don't see why, as long as the law spells out what reasons for the act are mitigating circumstances, and as long as investigators are objective in figuring out why someone acted. It's entirely normal to take motive into account in criminal prosecutions. If you punch someone in the face and he falls over and hits his head and dies, you're guilty of manslaughter. But a court is undoubtedly going to take into account why you punched him in determining the severity of the charges and sentence. If you punched him because he punched you first, they'll go easier on you than if you punched him because you demanded his wallet and he didn't hand it over.Stating a different reason for the same criminal act somehow makes it less severe or not severe is somewhat lacking in objectively.
Actually, if he punched you first and you punched back in self defense you might walk. You met force with like force, he was very unlucky. Too bad.
That said, the notion that burning a synagogue to protest Israel doesn't count as antisemitism is ludicrous. The perps didn't target their victims because their victims were part of the Israeli government. They targeted them because they were Jews. If the perp's thought process connecting his victim to the target of his protest passes through a "because he's a Jew" step, then, irrespective of whatever dumbass garbage comes before that step or after that step in his reasoning process, it's antisemitism. This is not rocket science. One might as well claim beating up a Jew because the Jews killed Christ doesn't count as antisemitism, provided the purpose was to protest the Crucifixion.
I see one way they could see it as anti-Israeli: They think all Jews are Israeli. I don't think that should give them an out on hate crime charges, though--the threat is just as real if they're targeting Israel and think all Jews are Israeli or if they are targeting Jews directly.
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It is possible that it symbolizes Israel to some people.
If a random building used by random German Jews to practice Judaism "symbolizes Israel" to someone, then any and all things Jewish are equated to Israel in that persons mind. That makes anti-Israel and anti-Semitic one in the same thing for that person. Their is only a distinction between the two for people who don't view something as symbolic of Israeli government policy just because it has a connection to Jews.
BTW, if they firebombed a building as a political act against the state of Israel, then it wasn't just a hate-crime, it was also terrorism.
I don't see it as terrorism. They're not trying to scare anyone, just trying to destroy Jewish things.