So the thing is, ludonarrative often works on the level of feeling. In Clint Hocking's Bioshock article, he's describing how the experience of playing Bioshock made him feel disconnected from its story because he felt the gameplay was giving him a moral choice (to be selfish or not to be selfish) but regardless the story was forcing him to be altruistic by trying to help Atlas.Casual Shinji said:That's not really a contradiction, since all the people he kills are "bad guys". Characters like Han Solo and Indiana Jones are still likeable and they kill tons of people, too.
Now, in a very literal sense I could argue that this isn't a contradiction because Jack is a brainwashed clone who is forced to obey Atlas' commands, and that is true. It makes sense that Jack has no choice to obey Atlas, but that wasn't Hocking's problem. His problem was that it felt wrong, on a visceral level.
Many, many people have pointed out a similar experience with the uncharted games. It's such a well recognized criticism that Naughty Dog have directly responded to it (a response I suspect you've read, given your examples) and added an achievement to one of the games. It doesn't matter why people feel this way about Nathan Drake and not about Indiana Jones, the point is a lot of people clearly do. Heck, the zero punctuation reviews of the series have always made a big deal of it.
One possibility is that it may just be a feature of length (a game is typically much longer than a movie and thus will in practice involve more people dying in more repetitive ways), or maybe it's a tonal shift between the cutscenes often looking like Nathan Drake's super fun gap year and then suddenly morphing into an 80s action movie as soon as bad guys show up, or maybe it's the fact that Nathan has a very different established personality (and generally seems to act like it's all a rip snorting good time adventure with occasional mild peril).
Summer Blockbusters use film language to deliberately steer the audience away from thinking about things you aren't supposed to think about. You can shoot a scene with someone mowing someone down with a machine gun, but you can essentially choose whether that scene is emotionally impactful or not by the way you film it. Games generally don't really have the same degree of tonal control, what they have instead is ludonarrative.