Yeah, it's like, in his (Kishi's or Naruto's) mind, "not killing" and "forgiveness" somehow always go hand in hand, so if Naruto chooses to forgive people like Nagato, Obito, Sasuke, etc., then that somehow means he's not allowed to kill them it seems like.
It's also why the Talk no Jutsu was so stupid half the time, especially when used on ones like Nagato or Obito. Nagato was a true, unfortunate victim of war and has seen the devastation first hand while also experiencing such treachery like by Hanzo and Danzo that resulted in his best friend's death, and then proceeded to spend decades completely entrenched in his beliefs, never questioning his actions, always seeing them as justified....until Naruto comes along...despite the fact that Jiraiya himself had tried to convince him otherwise....one pretty little speech from Naruto and Nagato is suddenly willing to just drop and forget it all just like that....and the only way the TnJ even has the slightest possibility of working is because a majority of Naruto's main antagonists have been "Naruto gone wrong" foils, all in hopes that the reader (and Naruto) would automatically sympathize with them and not want them killed (at least not as a result of a mere fight).
Any other time, you notice it's almost the opposite. Look at the enemies in the movies, for example, who aren't such foils. Naruto doesn't seem to have any qualms with killing them, and seems to even lack a lot of the helpful enthusiasm he has at other times. Like in the first movie (Land of Snow), he's actually a bit of a jerk to Koyuki much of the time and not looking eager to help her at all. Heck, when Koyuki asks him why he's always finding her and bringing her back (after bringing her back the 2nd time shortly before encountering the train, IIRC), he even merely says that it's his mission...that's it...not because he felt she was wrong for running away and should face her fears and not because he wanted to help the people of the land get out of Doto's hold, but simply because it's his mission...it's an obligation that he would avoid if he could have.
I want to see Naruto that TNJ on other villains and Fail with villains who are complete monsters, like The Joker, Darkseid, Thanos, Freeza, Cell, Beerus, Terminator , Galactus, Ra's Al Ghul, Red Skull, Loki, Apocalypse, Yhwach, Aizen, Grimmjow, Ragyo, Doomsday, Zod, Sinestro, the Anti-Montior, Freedy, Jason, Michael Myers, Kefka, Sephiroth, Garland, The Emperor form Final Fantasy II and Star Wars, Weseker, Let me know if a missed any.