"Geoff Keighley didn't tell those working on the show what he was going to say."
Keighley was asked about this speech (watch it above) as part of a Reddit AMA. Specifically, when asked what prompted him to make the announcement--something that could have been ignored during the show--he explained, "It just broke my heart that he couldn't be with us--something had to be said. I didn't tell anyone on the show team what I was going to say and it wasn't rehearsed."
Prior to the show, Keighley had sent out a number of tweets about Kojima, none of which indicated that he wouldn't be there. As for why he did this, Keighley said, "I wanted him to know that we were thinking of him. I was trying to do all I could to make him feel connected to the show, even if he couldn't be with us physically in LA. Heartbreaking situation."
Keighley also reiterated what he said during the speech, that Kojima was watching the awards from Japan. "Yes, he was watching it live in Tokyo with friends," he said. "He tweeted a bit during the show."
Following the end of the show, Kojima tweeted, "Thank you very much."
http://www.gamespot.com/articles/revelation-that-kojima-was-blocked-from-attending-/1100-6433094/
#FUCKONAMI