Film has distinguished itself as an art form for decades, far beyond what games have done so far. I might argue your choice of example auteurs, but still there are hundreds of directors whose films have more literary merit than any of your video game examples. And 'gamers' don't deserve to snort coke off of Roger Ebert's ****. At some point video games might achieve something that's worthy of the kind of literary depth seen here, and a reviewer/essayist competent enough to explore it (and that title certainly isn't without peer or superior).
The uncorrupted state of human relations is not tolerance and understanding. Social behavior, mores, and prejudices stem from systemic social needs. If these needs have be resolved without this behavior (child care, birth control), , then the behavior and mores will gradually vanish. But treating them as inventions with no basis in reality will not help reduce or suppress these leftover behaviors, but rather boost them. Teaching children that the stereotypes that they witness every day are non-existent is no way to help them deal with race, gender, or sexuality.
Misogyny is the hatred of women, despite what feminists have tried to morph the term into. Equating sexual objectification and paternalism with hatred is a shrill, hostile and weak position, and not one I think you are trying to take, so please change your terminology. Using the allure of an attractive female character to sell Alpha Protocol does not mean that Matt Rorie hates women.
The media does not create the social atmosphere, it reflects it and generally is restricted by it. It's currently reflecting a reality where homosexuality is accepted and normal, and women and black people can become president. With such a breadth of tolerance and respect for humanity as the status quo, one would imagine there is room to portray the human animal as it sometimes exists, such as a regional manager of a paper company unable to view an employee beyond her gender and appearance, an ad agency executive spying on his wife's psychotherapy, and a young secret agent finding his way into the bed of a powerful German mercenary who is turned on by danger-- all without accusing the creators of these works of harboring hatred for women.
And Bond, in Fleming's novels, is an actual misogynist. He's clearly disgusted by anything remotely feminine, and portraying today him as he was written would make Don Draper look like Margaret Sanger.