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 on 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."
Kilmarnock manager Kenny Shiels was delighted with the way in which his side played their football despite the difficulty of implementing such a strategy at this time of year. He also reserved praise and put the efforts of Heffernan into context.
Shiels said: "He's gotten the chances and he's put them away and you have to give him credit because you look at what he is playing against. It was a good outcome and the boys have showed good character again. To beat a club the magnitude of Hearts three times in one season is a terrific record for the boys.
"What you get in February every year is pitches that are not as fluent. That means there is a reduction in the passing volume you can achieve in the game. I was pleased with the way we passed it. I think we counter-attacked well. The dove tail in our co-ordination of the movement was outstanding."