Nekocat, are you reading a lot of classic literature...? This might not be the best representation of modern colloquial English, though I applaud your interest, especially in novels like Frankenstein, which sort of get short shrift due to their popularity in pop-culture, but there are very many subtle metaphors to that book.
It sounds like a Shakespearean or old English expression. It could also be worded, "Be it on your own head ......" But you wouldn't hear this anywhere in the modern world (except maybe in a few subcultures).
Well, not really 古い - most of the dialogue there is still everyday English. 'Be it' is still alive in today's 熟語. Usually it's found in the expression, 'so be it'.
In that dialogue, 'be it' is used to convey emphasis in a way that implies 'okay, but be prepared for whatever happens and don't say I didn't warn you'.
If you remove this emphasis from
'But on your own head be it if we have trouble from this scorpion, Wolff!'
it would become:
'But on your own head it will be if we have trouble from this scorpion, Wolff!'