Captain Kirk was not even in the pilot.
The pilot episode did not feature the emblematic Captain Kirk but another character who was scrapped from the script when the pilot was rejected. Producers had to fight to keep the series, but they had to change the plot slightly. It was then that the captain that all Star Trek fans know came to be.
Of course, this hand gesture means "read between the lines"...
He came up with it for the character. He's the reason it's in the show. That's all that anyone needs to know. Pointy ears weren't a new thing, either.