"She's absolutely staying with the show. There's an unbelievable story line for her this year, which is really central to everything that's going to go on this season," he told a meeting of the Television Critics Association on Wednesday.
Last month, in explaining why she didn't put her name in for Emmy consideration, Heigl said she hadn't been "given the material this season to warrant an Emmy nomination."
Nominations for the 60th Annual Primetime Emmy Awards were to be announced Thursday.
McPherson noted that Heigl won an Emmy Award for her role as Dr. Izzie Stevens for the previous season, then defended the popular series.
"It's unfortunate when there's any kind of turmoil on a show... I think it's a beautifully written, beautifully acted, beautifully produced show," he said, adding that all those involved with it deserve "an enormous amount of credit." "I never like to see when any of them are in any way taken lightly," McPherson said.
A spokeswoman for Heigl said the actress had no comment.
Heigl shot to box-office success last summer with the comedy "Knocked Up" and this year's "27 Dresses."
