I think it's a bad analogy in poor taste but I don't think it's particularly threatening. By that I mean I don't think you have anything to worry about the teacher being physically violent against your son.
I think the teacher was probably trying to get a point across but spoke before they thought.
Sounds like there is more to the story. When I was in high school yes teachers spoke like that, but not all the time and only when either they or their position was threatened. And it meant very little anyway. I would be more concerned that perhaps this wasn't an isolated incident (ie. they had done it before) or that perhaps the person he was with is a known trouble maker.
It sounded quite threatening to me and quite honestly, if it's enough to upset your DS and yourself then definitely speak to someone about it, whether it be the coordinator, the Principal or the Dep. Ed or all 3. Teachers shouldn't speak to students like that ever.
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