Since he has the position, I imagine he had input in the script-writing phase. Then again, it could be something minor: Millar recounts in the supplementary material for Civil War, that Whedon was the one who supplied an answer to a problem that the creative team was facing: namely, the ending. He told them that audiences craved a winner in a versus match, and hence they had to decide on who would win the fight (Cap or Iron Man.) Thus, the ending we know was reached: Cap won the fight, Tony won the argument.