It was the Ayrshire side's third win from three games against the Edinburgh club in the Clydesdale Bank Premier League this season, with Irish striker Paul Heffernan being the second Killie player to net a hat-trick at Tynecastle.
In the build-up to the game Hearts announced that captain Marius Zaliukas was likely to miss the rest of the season with an ankle injury and then watched on as the deputising Darren Barr was forced off after a clash of heads after 36 minutes.
It left the home side's defence somewhat of a makeshift unit but McGlynn was dismissive of any excuses for the defeat.
"It's a sore one for us to take," said McGlynn. "It is unacceptable from our point of view.
"In both boxes we weren't committed enough. Kilmarnock have taken their chances and we haven't taken ours.
"They've set themselves difficult to beat and we've tried to break down but they've scored on the counter-attack with a switch of play.
"We tried to change things around and look for the goal in the second half but we didn't defend a corner very well and we find ourselves 2-0 down.
"It was not the kind of defending we've been used to. Defensively there has been massive changes since the start of the season.
"Our goals against column has been good and our defending has been good. It didn't help having to change our defence so much, but we should still be defending better."