'over-scrupulously' is formed from the prefix 'over-' + the adjective 'scrupulous'. 'Over-' comes from Old English 'ofer' meaning 'above, beyond', and 'scrupulous' comes from Latin 'scrupulosus' (from 'scrupulus') meaning 'a small sharp stone' that caused unease.

'scrupulous' entered English via Latin 'scrupulosus' (and the noun 'scruple' from 'scrupulus') and came to mean having moral doubts or strictness; the productive English prefix 'over-' has long been used to indicate excess, producing 'overscrupulous' and its adverb 'over-scrupulously'.

Originally related to the idea of a 'scruple' (a small stone causing unease) and thus moral hesitation, the sense evolved to mean 'having careful moral or ethical standards'; with 'over-' prefixed it now means 'excessively conscientious' or 'too particular about minor moral/details.'