The 29-year-old was dropped as a judge on the ITV1 show after just six days.
"I had a long conversation with Simon after he flew back from LA," his publicist Max Clifford told The Mirror.
"I feel for her and so does he. It must be very upsetting [for her], and that's why he was very very keen to let everybody know that Kelly did everything that was asked but it was one judge too many for that format."
The model was axed after Cowell realised that the show worked better with just three judges, but may return on a different programme in the future.
"It was an experiment and Simon just feels very bad because it's been made to seem as if she failed and she didn't fail," Clifford added.
"He said to me this morning: 'She was good, Max, she was genuinely good.' Simon's always looking for new shows, always thinking about possibly doing this, possibly doing that and Kelly is definitely someone he would want to work with again provided there's the right format."
The new series of Britain's Got Talent will air on ITV1 in May.