First, if instead of 32,000, the meagre number of 3 was used, then the whole concept of the film fails. Saying that there is a secret love jihad conspiracy going on here, to forcibly convert girls and send them to ISIS, and as a result of this conspiracy, only 3 women suffered, then it means that these are individual cases. There is no conspiracy here.
Second, to generalize and exaggerate things to this level is simply stupid. If this was done with any other incident you will say that it is utter nonsense.
Let me use an example. Over the last few months, there were 3 such cases of an Indian citizen urinating on a co-passenger in an airplane. Now imagine, a country like America or Japan makes a film called The India Story and the film shows how Indians always urinate on co-passengers in airplanes.
32,000 such incidents too place where Indians have urinated on someone. How will you feel about it? You will say that it is utter nonsense. That they are trying to defame the country. But if on the other hand, the filmmaker says that 32,000 was an exaggerated number but it did happen thrice, so making the film was justified.
What would be your response in that case? Does it make any sense? Similarly, the entire state of Kerala is being defamed for 3 individual cases.