I wouldn't say it was anti-UN per se. The UN just happened to be the vehicle that bad guys used. It was ramping up an extrajudicial military force, coordinating with rich elites in the shadows and spreading a plague for political leverage that was the bad stuff (Paul was clearly against, but other characters not so much).

The good guys were trying to coordinate and make sure vaccine was widely distributed, and IIRC the original friends of the main character continue to believe in the value of UNATCO (the agency you work for in the game) and treat it like a good cause that was poisoned rather than a philosophical error.

I can see the libertarian bent, but with the very heavy qualifier that it's like Noam Chomsky 90s anarcho libertarianism than the joke that is today's fascist-friendly memeified online libertarianism. I doubt Tracer Tong and Alex Jones would have much in common if they tried to have a conversation. And it does give you three choices at the end of the day, and seems to mean it, though if you squint I suspect it's most sympathetic to Tracer Tong's preferred outcome.