The OED has a good explanation: “In later Old French serurgien, contracted surgien, whence English sirurgien, surgien, now corruptly surgeon. The Renaissance b

The OED has a good explanation: “In later Old French serurgien, contracted surgien, whence English sirurgien, surgien, now corruptly surgeon. The Renaissance brought back to French and English (partly also to Italian) the spelling chir-, but never to French the pronunciation with k, which has now established itself in English, largely because the word being no longer in popular use, the traditional pronunciation has yielded to a new one, founded immediately upon the Greek The original ending which would normally give modern chirurgian, was variously perverted in 16th cent., and finally settled down in its present form: compare surgeon n. The result of these successive re-formations and perversions is that the modern /kaɪˈrɜːdʒən/ is, strictly, a different word from Middle English /sɪˈrʊrdʒɪən/, though it would be difficult to draw a chronological line between the two.”