McKeown has not featured since early March and went under the knife to cure the problem.
Killie assistant boss Jimmy Nicholl said: "Rory McKeown had an operation yesterday. It seemed to be a success.
"It was just a wee clean-up, a tidy-up, but I think his season is over to be honest.
"The medical people might tell me something different but there are only four or five weeks left so I can't imagine Rory being involved."