I think it's impossible for a bunch of code to feel anything about anyone, at least in this day and age. And especially when the code was made more than a hear ago.
And I don't think we have enough here to fully know if the actual creators of the game actually feel hostility toward women. Games aren't books, they aren't made by one person, they're made by lots of people and approved by lots of committees before anything makes it into the final cut. So not all of these ideas came from one person's head, it came from many groups of people operating under the same rough guidelines of themes they felt were marketable in their game.
So what is marketable in games? Sexy women, of course. And what else? Oh yeah, violence. Slap these two together and you've got a winner, right? Unfortunately, combining these in such a simplistic manner leads to a lot of uncomfortable scenes and subtexts that the article there pointed out. A world where every female must either be sexualized or an antagonist (preferably both), which thus leads to some uncomfortable and frankly bizarrely sexual deaths and murders.
I do not think it was the intention of the game's creators to make a misogynistic murder simulator, but I think by haphazardly slapping together sexy women and violence that's rather what they got. And that's...not okay. It speaks to tone-deafness on many levels of their development process and a lack of thought and clarity in regard to their vision. So no, I don't think "Hitman Absolution hates women," but I think IO Interactive doesn't do a lot of thinking before they create. This is further exemplified by the Facebook App [http://en.wikipedia.org/wiki/Hitman_Absolution#Controversies] they made to promote the game. The app let you identify Facebook friends as targets of assassination, with such identifying traits being "her hairy legs" "her small tits" "his shit hair" and "his tiny penis." You could choose a reason for killing the friend, and send the friend you've killed a personalized video that splices together their pictures on their wall with Agent 47 shooting them. Needless to say, it was taken down the same day, with an apology from IO.