The Avengers writer/director said that Marvel Studios wanted Clark Gregg's S.H.I.E.L.D. agent to die from the outset.
The character will return in Whedon's S.H.I.E.L.D. television series.
"Coulson's death was mandated in the first meeting by Kevin Feige," he said during a screening of the film at the Directors Guild in Hollywood.
"I can't say that enough times. Apparently I have some kind of reputation that we won't discuss right now, but I do love to kill people. Clark himself said when we were shooting that it was obvious that it had to happen, otherwise all of this becomes irresponsible. There's no toll or actual downside to this very bad idea of bringing all of these people together.
"As a film it's just irresponsible. That's why we're bringing him back for a S.H.I.E.L.D. series."
Coulson was established as an original character in Iron Man, Iron Man 2 and Thor.
He later debuted at Marvel Comics in the Battle Scars miniseries.