Danny Boshell's brilliant volley and Hunt's strike put the lowly Mariners 2-0 up, before Dons skipper Keith Andrews pulled back a late consolation for the hosts.
Milton Keynes laid siege to the visitors' goal early on with some hi-tempo passing football, but after Izale McLeod had missed three good chances, Boshell hit the hosts with a classic sucker-punch at the other end to give Town a shock 32nd minute lead.
Tom Newey's deep cross found Boshell unmarked at the back post and he gave Dons goalkeeper Lee Harper no chance with a ferocious 12-yard volley inside the far post from an acute angle.
Milton Keynes battled back and the off-balance Dominic Blizzard headed Jon-Paul McGovern's cross over the bar from five yards, before Sean O'Hanlon headed set-pieces from McGovern and Dean Lewington just over the bar in the dying seconds of the first half.
The Dons threw on Leon Knight and reverted to an attacking 4-3-3 formation after the break in a bid to get back in the game, but Hunt's volley doubled the Mariners' lead in the 53rd minute.
Ciaran Toner's corner was only half-cleared by the Dons' defence and the unmarked Hunt volleyed the ball back through a crowded box and into the net from 15 yards.
Grimsby midfielder Paul Bolland should have made it 3-0 but he was denied one-on-one by Dons keeper Harper, before Andrews pulled a goal back in the 71st minute.
Andrews swivelled ten yards out to fire into the corner after Knight and O'Hanlon had seen their shots blocked.
Town substitute Peter Till belted a 16-yard thunderbolt against the bar, while McLeod blazed over a great 15-yard chance to equalise for the Dons in a frantic finish.