It's pretty simple, really. They tried to tell the judge what she was and was not qualified to comment on. They tried the same stunt with the other guy too... which didn't work out too well for them.
Simply put, you don't get what you want out of the justice system by trying to tell the judge they're not allowed to do something, esp. when it clearly is within her purview...
Finally, you're forgetting that they've already lost... they're guilty. The only question is the punishment. Personally, I think that KK is going to rip Ashcroft's DoJ a new one for the anemic agreement they came up with.
There's one other issue to consider as well... the marketplace. Between 09/11 and Enron, people are feeling a lot less tolerant of the kinds of shenanigans that MSFT (and many others) have been getting up to over the last fifteen years or so. I think you (and the marketing mavens at MSFT) are about to get very surprised by the paradigm shift that's occurring right now in the zeitgeist of the marketplace.
While we're on the subject... you might to well to consider the damage that MSFT and its behaviour has done to US competitiveness in the global marketplace. A lot of countries are trying very hard to get away from MSFT, because they don't trust them and they don't trust their products. The free ride that MSFT seems to be getting from the regime (not the justice system, the regime) only emphasizes those trust issues in their minds... and extends those trust issues to the US as a whole.