If in the Maze Runner the Kill order, the Disease department developed a new disease to control the human population, wouldn't they have come up with a cure just in case?
It has not been explicitly referenced in the two movies at this time. That said, from the book, it was clear that it was not meant to be the maniac creator it became.
The disease, virus VC321xb47, was designed to kill quickly, without turning people in cranks. It was also supposed to slowly get less infectious as it progressed. It had a built in expiration. But when released, it quickly showed that it did not work as expected.
Since the virus was meant as a killer, a cure is pretty much pointless. Like shooting someone with the hope you can fix the organs afterwards. It is also against the idea behind the virus, which was meant to kill half the population of the planet. No cure, nothing to stop that from happening.
As it's implied the virus mutated, then a cure likely wouldn't have worked anyway.