After John Wick burned the chapel, he had a chance to kill Vigo when he was looking at Vigo from the top of the building, and then quickly went downstairs to intercept Vigo. He also shot the bodyguard around Vigo first without killing Vigo first... Obviously John Wick wanted to capture Vigo and force him to reveal his son's whereabouts.
To sum up, John Wick and Vigo are both given a chance, not a plot bug. It means that John Wick is very disciplined and only targets the parties...
Personal opinion, if you don't like it, don't spray it.
View more about John Wick reviews