All observed resistance mechanisms (so far) work via active counter-measures, such as additional ion pumps, and they reduce the fitness of fungal cells as a result.

No, if it allows the organism to survive, it increases fitness by definition. "Survival of the fittest" does not mean "All those fungal cells who went to the gym and ate right and look like Arnold Schwarzenegger get to live because they are so beautiful." It often means the equivalent of drug addicts on skid row, so long as they live longer with the "bad" choice than without it.

Sickle Cell Anemia reduces fitness compared to people without the disorder -- unless you live someplace with malaria and no effective treatment for it, in which case you live longer if you have Sickle Cell Trait than if you don't and, gee, too bad, so sad that having two copies of the gene is so torturous and debilitating.

Survival of the fittest is a war of attrition. It's last man standing no matter how awful he looks or terrible he feels.

It's not we can build a better organism if we plan this in advance, one that is stronger and faster and prettier.

Wrong. Or rather, needlessly obtuse in the clear context under discussion. The fitness function for human pathology is replication in excess of the body's capability to control/react adequately to maintain health. There's multiple counter factors going on. If an adapted resistant organism replicates 100x slower such that the immune system is then able to keep up and eliminate it, and/or the probalistic function drops below sustainment, then while yes it's successfully more fit vs the chemical compared to the vanilla organism from the perspective of patient health that's a huge win and the adapted organism has greatly reduced "fitness" (infectiousness/pathology) vs vanilla. The drug has done its job both destroying the vanilla and reducing danger of resistant, effectively driving evolution towards something more stable for humans.

We don't need to avoid all organisms in our bodies, we merely need to avoid harmful ones that damage/destroy the host vs live with it to an acceptable degree (or even have mutual benefit). Some adaptions to some drugs don't have any effect on the pathology of the infectious agent, so they can resist it "for free" from a health perspective. If others mean the resistant is less dangerous than wild type that's good.

I'm not really sure where the whole movie analogy stuff comes in.

In practice, the body is the battlefield and using very strong (toxic) drugs to pursue a scorched earth policy type health agenda tends to cost humans more than it costs pathogens.

If you successfully ruin this pathogen but also ruin the host, something steps in and that something tends to be something we cope with even less well, much like many Native tribes were decimated by "common" European diseases upon initial exposure because they had no immunity.