The film's reception was so bad, the G.I.Joe film's ending was hastily re-written as they were also planning to "subvert expectations" by killing off the boss character.

It was G. I. Joe's fault in the first place.

Buzz Dixon, a writer for the G.I. Joe cartoon, revealed in an interview that Duke was indirectly responsible for the first death of Optimus Prime, who in turn was indirectly responsible for saving Duke's life. The writers of G.I. Joe: The Movie asked Hasbro for permission to kill Duke off, and Hasbro not only granted it, they thought it was a great idea and way to clear out older characters in favor of new ones, so they instructed the writers of the upcoming Transformers movie to kill off most of the original cast of the cartoon series. The Transformers movie ended up being released first, but fan (and parent) reactions to all of the character deaths, especially that of Optimus Prime, were overwhelmingly negative, to the point where a spooked Hasbro changed their minds and ordered the Joe writers to spare Duke. This led to an awkward new dialogue in the G.I. Joe movie stating that the clearly killed Duke had merely fallen into a coma, along with an inserted line at the end saying that he had awakened and was going to recover.

THAT'S THE CORRECT RESPONSE. They didn't "double down" like what they do today.

They literally did the exact same thing with the second live action movie and killed off Duke [again]. Nothing was learned.