I am confused.
The particular Bible passage was written in Greek a solid millennia before Hogwarts was built, it was available in Latin at least since the 4th century (Latin being the language of the educated post-Roman Empire, and the language which magic seems to be based off of), and, according to a quick Wikipedia search, translated into Old English by the Venerable Bede in the 7th century.
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It's a fairly literal translation. I think the most likely option is that the Potter motto was first taken from the Bible in Latin, and at some point after the completion of the King James Bible (in the 1600s) the motto was updated to English.
The Peverells were, after all, contemporaries of Godric Gryffindor (at least in the HPMoR universe), so they would've been all over the Latin mottoes.
The motto is in Old English in the story, presumably dating from the time of the Peverells. It may have been taken from the bible verse, but then your own argument raises the question, why didn't they write their motto in Latin?