In French, 'tête', meaning head, (teste in Middle and Old French) has a more physical connotation, and while sharing many English uses such as the lead, or front of something, typically 'esprit' is used to refer to one's mind. French phrases that do use the word 'tête' in a similar fashion to English tend to have physical connotations, for example 'avoir la tête dure', to have a hard head, or 'avoir la tête sur les épaules', meaning 'to have the head on the shoulders'.
Consider that French has had a profound impact on the English language from Norman invasion in the 11th century BC, whereas public acceptance of neuroscience, and thus the conception of 'head' in a non-physical context is a fairly recent thing. If you consider the implied physicality of the phrase in question, it would appear to divide this apparently clash of connotations into two distinct meanings.