"Take an ounce of dried orange-peel finely powdered, divide it into scruples, and take one scruple at a time in any manner" is a remedy advised by Samuel Johnson for indigestion and 'lubricity of the bowels' (taken from the recently published Wits and Wives: Dr Johnson in the Company of Women, by Kate Chisholm, page 129). Clearly 'scruple' here has a different sense from the usual meaning today (moral qualm).
A scruple was originally (late 14th century) a small unit of weight, as used by apothecaries. It was also used as a term of measurement in other contexts, eg a scruple was a sixtieth part of an hour, or a minute, but was also, confusingly, a sixtieth part of a day, or 24 minutes. By the late 16th century 'scruple' had come to mean any small amount or quantity. Scruple is believed to have its origin in the Latin word for 'small pebble'.
The other meaning of 'scruple' has a separate entry in the OED, but this sense, too, is believed to be from the Latin for 'small pebble'; Cicero used the word scrupus to mean a cause of uneasiness. If 'scruple' or 'scruples' is in a sentence, it is usually accompanied by a negative word such as 'no scruples', or 'without scruples'. The adjective derived from it, 'scrupulous', too, is less common than 'unscrupulous', and although 'scrupulous' is common enough, again it often comes after words such as 'not', 'less' or 'less than'.