I believe you will find the nuance expressed by the progressive here addressed at this question: where the simple construction asserts the fact of the action, the progressive ascribes a character or quality to it.
This use is typically found in contrastive situations like that in your example, where the speaker/writer is concerned to draw a distinction between two interpretations of an event or action:
He wasn’t serious, he was just joking. (not "he just joked")
The contrast often addresses a distinction of motive, and it may be that your writer is saying that President Clinton's intention was to save Pakistan rather than India; but I think it more likely that the writer means that if Pakistan had nuked India India would have responded with such ferocity that Pakistan would have been destroyed.