It is strange that a retired Navy captain was so reluctant to assert his authority. At first he just didn't want her screwing up so badly, but by the home stretch, as the movie shows, he was genuinely afraid of ticking her off.
By the time she was announced and gained popularity through her looks and folksy ways it was too late to reign her in. McCain was going against the political powerhouse that Obama was back then.. a charming, intelligent (and admit it or not.. african american because it was a huge factor with minorities and the african american communities) man and McCain couldn't afford the slightest public hitch in his campaign because he was already on the ropes as old whitey.
As time progressed and Palin become more erratic and self-assertive it was already way too late. She was a very public figure and replacing a VP candidate was unheard of and would have immediately sealed the campaign for McCain.
So it was smile through clenched teeth and hope for the best and the movie portrayed that perfectly.