First, Harry discovered a gag beverage that he thought could be a key to power, although he quickly realized the Comed-Tea wasn't as powerful as it seemed. A few days later he fell in love with a device that is sometimes given to students who want to take extra classes, although he has since discovered some limits to its powers. If he goes rogue over his Time-Turner's crippleware, then who knows how much other cool and useful magical stuff he will miss out on, and how much trouble he'll be in.

Plus, McGonagall had him cornered when she confronted him about returning the Time-Turner - whatever he tried to do, she'd see it. Also, McGonagall had earned some degree of trust & respect from Harry, she's correct about Harry repeatedly misusing the Time-Turner, and she'd already warned him that they'd take it away. So it's not unreasonable to go along with the punishment, and try to earn her trust back so that his Time-Turner can be restored later on.