Because the Justice Department is part of the Executive Branch, there is little chance it could ever be completely independent of executive power. I know this is a common mistake. There are three branches to our federal government. They are the legislative (Congress), Executive (President and federal agencies) and Judicial (primarily the Supreme Court). The Department of Justice is headed by the Attorney General, who is appointed by the President, confirmed by the Senate, and is a member of the Cabinet. The Department of Justice includes law enforcement agencies like the FBI and also includes the federal prosecutors who went after Microsoft.

From my perspective, the Microsoft case has reeked from the beginning. It was instigated by Microsoft's competitors who incidently were major political campaign donors. Microsoft made the foolish mistake of thinking they didn't have to pay bribes to politicians in order to do business. As a result, they had few friends in Congress or in the Clinton administration. As a result, few in power spoke up for Microsoft when the government went after the company.

As for suing governments, there is a long-held policy known as sovereign immunity that makes suing a government very difficult. Sovereign immunity dates back centuries when kings justified their power in the name of God. I personally think sovereign immunity has been abused but I can see the can of worms it would open if anyone was free to sue governments at will.