How did Discovery justify the Federation's gunboat diplomacy toward the Klingons? I know the Klingons were supposed to represent Trump supporters with their isolationist attitude, and thus the writers assume we'll see them as the bad guys. But aren't they a sovereign species? Don't they have a right to self-determination? Forcing them to open their borders makes the Federation into imperialist bullies.
WANING! MAJOR SPOILERS BELOW!
You know, I never once got that this was supposed to represent Trump or his policies. This is, to be honest, media bias trying to stir the pot. Anyone who tries to make that claim clearly didn't watch the entire season or has an EXTREMELY biased point of view. Not once while watching the show did I ever even consider any parallels to Trump; the only correlation would be the fact that the Klingons are isolationists, which definitely isn't unique to Trump or the current US administration. It could be Russia just as soon as it's be Trump. Let me tell you why and how...
In the pilot, the crew goes to investigate a derelict ship near the edge of Klingon space (but still entirely in the Federation). They have no idea it's a Klingon ship but can't get close to it, so the protagonist, Michael Burnham, takes a space suit with a jetback and flies over to investigate. While exploring the external hull, a Klingon comes out the ship and attacks her, and she kills the Klingon warrior in self-defense (almost accidentally).
Thus begins a stalemate between the two ships: Klingon versus Federation. Michael Burnham wants to avoid war and has a telepathic link to Sarek (Spock's father; the how of this is later explored in the series), and Sarek tells her that the Vulcans avoided war with the Klingons by simply striking first. By killing the Klingons first on a sizable scale, they won the Klingon's respect and the Klingons knew not to mess with the Vulcans. Thus, Michael Burnham is led to believe that the only way war can be avoided is to blow up the crippled Klingon ship first, winning the other Klingon's respect. However, the Federation policy is never to instigate and always seek a peaceful solution, so Burnham's captain refuses to fire first, preferring diplomatic peace.
As a result, a frustrated Michael Burnham tries to stage a mutiny to destroy the Klingon vessel, essentially going against the spirit of communication, peace, and diplomacy of the Federation. This is why she is viewed negatively by the rest of the crew for much of the season.
Bunham ultimately fails, more Klingon ships arrive, more Federation ships arrive, and full on war breaks out. This sets the story in motion and is the catalyst for all of the series that comes after. There are massive casualties on both sides and Michael Burnham (who is a female btw, despite the name) is arrested for mutiny and sentenced to a Federation prison.
Just to add more context of this event -- we later learn that the Klingons, as a species, are essentially constantly in disarray. The great houses that control Klingon culture are always fighting for power, and the government isn't very stable overall. One of these Klingons, a great house named T'Kumva, wants to unify the Klingon great houses, seeing the Federation and their inter-species unity as an ideological threat. Thus the isolationism (which has ALWAYS been a theme of the Klingons; in fact, they were based as a parallel for the Russians during the Cold War). T'Kumva prefers complete isolation, fearing that contact with the Federation will dilute and destroy Klingon. The only way to save the Klingon way of life, then, is to unify the Klingon great houses ("stop fighting each other to save our way of life, and the only way to unify is to have a common enemy").
Thus, we eventually learn that all of this was a prelude to war -- the Klingon vessel was merely powered down and looking for an excuse to fight the Federation, wage war, and unify the houses. It was all intentional on the Klingon's part.
As for the Klingons as villains, they definitely do not paint the Klingons as outright villains. There's a few that are good and want to stop the war. In fact, by the end of the season the Federation is the villain!
Late in the season, there is a time jump and it's at the tail end of the war. The Klingons are winning and the Federation is about to crumble entirely. As a result, the Federation has decided to bomb Qo'nos (the Klingon homeworld) and completely wipe out the species (or at least the majority of them). The Discovery crew are unknowingly assisting in this, not realizing that they are delivering a WMD. Once they realize, however, they ally themselves with one of the Klingons that wants to preserve the Klingon way of life, but doesn't think destroying the Federation is the right way.
As a way of stepping out the situation, they give the good Klingon the detonator for the bombs and lets her do what she wants. She then essentially blackmails the other great houses, threatening to kill all of the Klingons if they don't put aside their petty internal bickering. She thus fulfills T'Kumva's original request with the need for destroying the Federation. She unifies the great houses under her fearful rule, but she also ends the war and allows the Klingons to continue in their nationalistic ways, which is where we find them in the original series with Captain Kirk and co.
The thing I'd like to point out about DIS is that all of the characters are various shades of morally grey. They forego the utopian idealism of TNG and show that even the best of characters can make questionable and bad choices in the name of good -- it's all about vantage. I think just about every main character on the show has to make those tough calls -- cannibalism (yes, really), illegal genetic manipulation (on both Federation and Klingon sides), torture and sexual abuse, sabotaging the Federation war efforts in order to save a neutral species, etc. No one on this show finishes the season with a squeaky clean palette, except for maybe Tilly, and even then she got to party hard with illegal(!) drugs.
I know that's long winded. Suffice to say, the writers may have been anti-Trump, but by no means was that reflected in the show at all in any way I could detect.
That explores the main content and question regarding any potential parallels between Trump and Trek. It was no more anti-Trump than, say, Star Trek Into Darkness, DS9's covert Federation war efforts (with Sisko even lying about certain events to get the Romulan's to join the war effort), TNG and VOY's potential genocide's against the Borg, etc. The thing about Star Trek is that the Federation is still fallible, and it's only by a few good people drawing their line in the sand that a better future is rewarded. That's ultimately the lesson for all on Discovery.
There are episode-specific themes that I touch on above (cannibalism, genetic manipulation, etc). That ties back into the spore drive and all that jazz. I can gladly go into it with you, but doing so would have sidestepped the bigger conversation piece about the Klingons.
TLDR; Klingons were bad, then Federation is bad, in the end we all suck but can overcome it with cooperation.