I wouldn't worry too much about it, as long as he recognizes good and bad in real life.  In the context of fictional worlds, such as those of superheroes, one can admire the villains for various "powers" or abilities that they have without losing a sense of right and wrong.  It's more like a battle between "cowboys" and "Indians" where you're not too focused on who's "good" and who's "bad" but on pitting their different types of skills and fighting styles against one another.  In a video game, for instance, one might enjoy shooting up some bystanders in the game, while never daring to do so in real life.  In real life, I have a hard time kiling a bug if I don't have to, but have no issues mowing down fake "pixels" on a screen (although I haven't played video games in about 25 years for more than 30 seconds at a time) ... precisely because I realize that it's not real.  So if your son doesn't have any issues distinguishing between reality and the fantasy of a fictional world or a video game, I wouldn't worry too much about it.