There are four main problems with this study that I see:
1) Bruce Bartholow states that people who regularly played violent games before the study "are already so desensitized to violence from habitually playing violent video games that an additional exposure in the lab has very little effect on their brain responses." It is implied that these individuals became accustomed to violence 'through' video games, and not as a result of other factors. We must consider that some people were less reactive to violence prior to playing games, and thus, were able to find appeal in games such as Call of Duty or Hitman where others are not.
2) What is the base level of sensitization for violence? Violence exists within the lives of all living creatures, whether killing for food, trying not to become food, protecting territory, or fighting over a mate. What is the 'natural' level of acceptance of violence? Are gamers really becoming desensitized to violence, or could it be that other people have become oversensitized?
3) Bartholow's study is limited to short-term effects. Will a person who witnesses violence be desensitized immediately afterward? Of course. Then again, we don't expect someone to immediately laugh as hard at the same joke or jump at the same frightening sound, but we know that the response may be reproduced again with time. Under Bartholow's assumptions, we should probably also shield our children from comedy for fear of turning them into miserably unhappy wretches through desensitization.
4) According to some of the surveys that Bartholow cites, "the average elementary school child spends more than 40 hours a week playing video games." So, considering that the average elementary school child also has time for homework, meals, using the bathroom, perhaps sports or music practice, and television shows, where do these supposed 40 hours come from? That's almost 6 hours per day. Are we to assume that the average kid is skipping school as well, or that the average kid stays up for two days straight every weekend? I think Bartholow might want to check the sources and practices of those surveys.