I believe the general trend in the American Media has been to keep plot and characters simple. As long as this is true, there will be a need by writers to use negative stereotypes. This stereotype may be the unethical, greedy businessman (offening people in the business world), a Pagan using “black magic” (offening Neo-Pagans and Wiccans), or any racial stereotype (obviously offending that particular racial group).
I see two solutions to this problem. The first is to take a sort of sci-fi approach and either create alien races or meta-humans (genetically modified or somehow superhuman) who would then take the role of “bad guy”. This approach is only a temporary solution, as aliens or meta-humans have a rare possibility of becoming a real part of our society in the future. In that case, this entire argument would be back to square one, with mainstream society subjugating the new members of society.
Solution number two (and without a doubt the better solution) would be for writers to create characters who are complex. A “bad guy” who is shown to have good intentions, or believes that what he is doing is somehow in the right, is much easier to sympathize with. A truly human and “grey” character would offend less people when given a specific race and gender. In addition, grey characters show people that any one person is a blend of stereotypical “good” and “bad” and never one or the other (as our current media portrays).