James Stewart is 'the bad guy'
Ok, bear with me.
Due to the ambiguous ending - guilt or innocence is never firmly established - I started thinking about the motives in the movie, and I'm leaning more and more towards thinking James Stewart plays the ultimate 'bad guy' in this movie, an unethical lawyer, not seeking justice, but just trying to get his client of the hook, using every trick in the book.
While Preminger is manipulating the viewer into seeing the prosecution as the scheming, arrogant, high-profile government officials, it's actually James Stewart who is manipulating facts, manipulating testimonies and badgering witnesses more than the prosecution is.
He constantly lets shine through that he is not convinced of Gazarra and Remicks innocence, but never really seems bothered by this. Even in the end when Remick and Gazarra have fled the scene he is not in the least worried that he might have set guilty people free.
Also some other moments, like the way he 'bribes' the judge in the judge's chambers by cosying up to him and giving him a fishing fly (hidden in a law book!), are clear indication that he is not driven by finding justice but by wanting to win the case. Also the 'greed' with which he is looking forward to his new case - representing the Quill estate - doesn't really make his character sympathetic.
If this was Preminger's intention then his casting choices were extremely interesting and pretty brilliant.
voting history: http://www.imdb.com/mymovies/list?l=629013