Dude, Goodell isn't ordering anything. You know what the absolute worst thing for the league, and by extension, him, would be? If there was anything at all that gave people another reason to stop caring about NFL football. The shitty performances in this post-season, so far, have to be bad news for the NFL. Now, they get a chance to redeem it all with a good Super Bowl. Some obviously half-assed bullshit penalty to hand the game to the Falcons would cement this postseason as a total loser for the league. Nobody, not even Roger himself, wants the story in two weeks to be "Did the Patriots get hosed because of Deflategate?"
Also, more generally: neutral and casual fans (who will be the vast majority of viewers) hate flags. It slows the game down and calls the game into question. That's my pet hypothesis as to why playoff games are more hands-off than the regular season, because the ratings are a lot higher and the game flows better. It's a showcase for fans that demonstrates the way football "should be" or "used to be" or whatever. People get a taste of fun football before the long spring/summer break, and that's what sticks with them through the offseason. And the league really wants this to be a good game, not a flag fest.