Can one use:
1) If he thinks that you broke his vase, even accidentally, he will beat you up.
2) If he thinks that you broke his vase, even if he thinks it was accidental, he will beat you up.
As with many of your sentences, navi, there is potential ambiguity. but most native speakers do not have a pedantic turn of mind. They let common sense be their guide.
I find "he will beat you up" a bit "schoolboys in the playground". I can't imagine any adult native speaker saying that.
"Invading armies have no rights." Noam Chomsky
I don't find "he will beat you up" at all childish, at least not when it's used metaphorically. Perhaps it's more common here in the States than in other Anglophone countries.
I am not a teacher.