McGlynn was forced to field a makeshift defence with captain Marius Zaliukas possibly out for the season due to an ankle injury and Darren Barr was then forced off following a clash of heads on 36 minutes.
Irish striker Paul Heffernan took advantage and helped himself to a hat-trick as Killie claimed their third win in three games against the Jambos.
"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."