Ela estava acostumada a não ser reconhecida em sua forma de gato
Como observado por Gallifreyan, o artigo de Pottermore afirma claramente que ela estava registrada antes de se formar em Hogwarts, e com a ajuda de Dumbledore.
By the end of her education at Hogwarts, Minerva McGonagall had achieved an impressive record: top grades in O.W.L.s and N.E.W.T.s, Prefect, Head Girl, and winner of the Transfiguration Today Most Promising Newcomer award. Under the guidance of her inspirational Transfiguration teacher, Albus Dumbledore, she had managed to become an Animagus; her animal form, with its distinctive markings (tabby cat, square spectacles markings around the eyes) were duly logged into the Ministry of Magic's Animagus Registry.
Pottermore - Professor McGonagall
Então por que ela ficou surpresa? Porque ela estava acostumada a usar essa forma para passar completamente despercebida por todos, exceto ela, os Aurores com quem trabalhava. Embora ela estivesse perto de Dumbledore, ela não estava trabalhando para a Ordem na época.
Minerva McGonagall did not teach the young Tom Riddle, but she was privy to Dumbledore’s fears and suspicions about him. Minerva was not inducted into the Order of the Phoenix during Voldemort’s first climb to power (at that time the Order of the Phoenix was seen as a renegade outfit by the Ministry; successive Ministers feared Dumbledore’s charisma and magical talent, and were inclined to harbour fears that he wished to succeed them). Minerva’s abilities as an Animagus were to prove useful in these dark periods of wizarding history, however, and unbeknownst to her students she spent many nights spying for the Ministry in the guise of a tabby cat, bringing the Aurors crucial information on the activities of Voldemort’s followers.
Pottermore - Professor McGonagall (behind paywall)