Murphy said Monteith's character Finn Hudson will not die of a drug overdose, which killed the actor at the age of 31 in Vancouver a month ago.
"There were a lot of things that we had to decide (for the memorial episode)," Murphy said and one of the puzzles was how Monteith would be written off from the story.
Murphy said they may end up not revealing the cause of death in the show.
"That might be weird for some people but it felt really exploitative to do it any other way."
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Murphy said Monteith's costars - including girlfriend Lea Michele - have been busy over the last couple of weeks with the first two episodes of the season.
"After that, we're going to take two weeks or three weeks down to get our heads together because it's been a really hard thing to write. We loved Cory and we loved Finn and it feels like a huge loss and a huge heartache not to have either of them around.