It's very unlikely that they actually did desecrate a Quran. Usually these things simply get made up to discredit someone that the accuser has fallen out with.
And the local population, nearly always poor and uneducated, lap it up because of their ingrained bigotry against those whose beliefs are different to their own. "Typical sort of thing an unbeliever would do" etc.
In more general terms, the kind of extremism that makes this possible is quite common in Pakistan. Which is a result of the Wahhabi-funded Madrasas which are all over the country, but particularly in poor areas, where the population are illiterate and have had no education to speak of, aside from what they received in the Madrasa (if you can even call that education).
I might sound like a broken record always blaming the Saudis for this kind of stuff, but their extreme brand of Islam, and the huge amounts of cash they put into exporting it wherever they can, is responsible for so many terrible things.