So in-universe the film wasn't racist to kill off Slipknot, but out of universe, we are to assert the writers intended harm to the Native American community by killing of Adam Beach's character? Sounds like a big stretch and something you put more thought into than other people who accused the film of racism.
I think "racist" is becoming an overused word. Just because something is "not as completely diverse as we would like it" doesn't mean that it's "racist." Should there be more depictions of Native Americans in superhero films? Absolutely. But that doesn't mean that it's racist to kill off a Native American character in a superhero movie. Not every movie has to be all things to all people at all times.
But then, I guess, welcome to 21st century Western Civilization, where some people view every interaction & every artwork as a tribal zero-sum game where the only way for one group to "win" is for another group to "lose."

Not like those X-Men films, am I right? Why Singer insist on having Mystique strutt around naked, is beyond me. It's certainly not something the character does in the comics, and JLaw has voiced her discomfort with it. A white dress Bryan, that's all I'm saying.
There is a certain internal logic too it. Since her one & only power is for her skin to change to impersonate other people, clothes & all, her powers kinda require her to be naked, otherwise it would look weird.
But then, the last scene of X-Men: Apocalypse would seem to address your concerns.
Paramount had a tough summer for sure. All their big name IPs under-performed or out right flopped. GB, STBeyond, TMNT 2.
While Paramount does currently own Star Trek & Teenage Mutant Ninja Turtles, Ghostbusters is a Columbia property.
witness, for instance, Tim Burton's consistent failure to include persons of color in his films.
He made Harvey Dent black. Jus' sayin'.
Katana is fixated on her dead husband and has next to no personality otherwise;
So, by that logic, the Punisher has no real agency either because he's just a mopey guy who kills people because he's fixated on his murdered wife.
For that matter, shouldn't we then be complaining about how Katana's husband not only didn't have a name but didn't even manage to have any screen time? He's a character that only exists to be killed in order to motivate another character!
There was no glorifying abuse or mistreatment of women. There was no "endorsing" these actions. No good guy came along and said "these actions are okay."
On the other hand, Bruce Wayne did show up at the end and agree to help sweep Amanda Waller's misdeeds under the carpet in exchange for information on the other Metahumans she's aware of.
Speaking of Bruce Wayne, where were Batman, Wonder Woman, & the Flash during all of this? We know that they are currently active superheroes at this time and this crisis apparently went on for 3 days, enough time for them to get to Central City if they were so inclined. So why didn't they show up to help?
I don't remember exactly how things played out in the movie, but could the whole thing with El Diablo be compared more to an accidental shooting or something like that.
You could make an argument that El Diablo is akin to Bruce Banner, someone who's powers can be unintentionally destructive if he doesn't maintain self-control.
Also, considering most of the protagonists in the movie were criminals, the fact that Diablo was the only repentant one should count for something.
And while it wasn't mentioned on screen, Diablo's wife did have a name in the credits. "Grace," I think.
As for Harley Quinn's relationship with the Joker, I would argue that it's not abusive. It's consensually sado-masochistic. Yes, the Joker is a crazy bad guy but so is she. They're evenly matched on that score.
Random observation: While rewatching the movie this afternoon, during the final battle, I noticed that Killer Croc has nipples.

