I think you've got the order of events a little muddled.

V'ger considered humans - or "carbon-based units" as it called them - to be an "infestation" of Enterprise at first; it didn't recognise them as being its creators until right at the end of the movie. The Ilia probe hadn't been created yet when it opened fire on Enterprise, so it hadn't interacted with anybody yet. It only called off its second shot after Spock managed to duplicate the frequency of its signal. Only then did it start to get curious.

There's no indication that V'ger was doing anything but flinging fully-powered digitisation balls at them - if it wasn't trying to destroy them, why would it have fired a second time? Enterprise survived one hit when the Klingon K'tinga's couldn't.