Microsoft was forced to pay a large fine and significantly change their business practices. The goal was never to destroy Microsoft, and even if the government could have somehow done so that wouldn't have benefited consumers.
At the start of the trial, Microsoft "only" gave about $10K to political campaigns. By the end, they were giving $1M to BOTH parties each year. This was the real problem. The government extorted them for political cover. And it's not like they were picking on them; they just forced them to start paying into the system in proportion to their success, like everyone else is expected to at that level.