The short answer is they came that way from the Latin. Excusare meant pretty much the same thing in Latin as it does in English. Recusare has drifted a bit from its Latin meaning of 'refuse, decline, be reluctant.' It also had the legal meaning of 'object, plead in defence [sic].' Does it help if you think of the ex- as meaning 'out of', not 'formerly' and the re- a an intensifier, not a duplication?