I read that completely differently. Much more as commentary on the drones, which have been a pretty hot topic the last few years, with a lot of innocents killed, but also a lot of bad guys.
If it had been an actual hashing out of issues (as in finding the good both sides are trying to do) I would’ve had no problem with it. If it had just been one line zingers (like in Avatar, Captain America, Iron Man 3) I would’ve rolled my eyes and moved on. As it is, Khan is portrayed sympathetically (!!!) and the big bad military guy is ... Well big and bad and connivingly evil. Until big bad military guy is (justifiably, mind you) killed by Khan and the Khan plays the bad guy... But only because he wants Starfleet utterly destroyed (and maybe kinda sorta all genetic inferiors but that’s only speculated by the characters... Khan never says that himself)
More simply, both the Admiral and Khan were pursuing personal vendettas (the Admiral wanted was to defend Starfleet and Khan wanted war to defend his people) but Khan’s (the terrorist’s) was given moral justification because... Well because... Without rationale... Slap a 9/11 veterans dedication at the end (which, after this movie, is really saying - sorry you guys had to go to go to war for a lie but we love you anyway) and the rationale becomes obvious...
And it ticks me off because Iraq was **and still is** an issue that’s even going on for 20+ years... And so this entire movie is a simpleton regurgitation of propaganda... And we’re bordering on the Liberty Valance effect...