A scruple can be a doubt, hesitation or unwillingness to do something due to uncertainity about what is right, or to show reluctance on grounds of conscience [source].
When scruple first appeared in English in the 14th century [source], it referred to a unit equal to ¹/₂₄ of an apothecaries ounce, ⅟288 of a pound, twenty grains, one third of a dram or 1.3 grams. As a liquid measure it was ¹/₂₄ of a fluid ounce, ⅓ of a fluid dram, 20 minims, ¼ of a teaspoon, or 1.23mm [source]. It could also refer to a minute part or quantity of something.
By the 15th century a scruple was “an ethical consideration or principle that inhibits action” or a “mental reservation” [source]
Scruple comes from the Old French scruple (scruple, compunction, qualm), from the Latin scrūpulus (a small sharp or pointed stone; ¹/₂₄ of an ounce; uneasiness of mind, anxiety, doubt, trouble; scruple), a diminutive of scrūpus (a rough or sharp stone; anxiety, uneasiness).