Complex sentence: The Pakistani military had prepared for the operation long before, and the government prepared for a three-front operation: isolating targeted militant groups, obtaining support from the political parties and saving civilians from the backlash of the operation.
Split into simpler sentences: The Pakistani military had prepared for the operation since long before, whereas the Pakistani government prepared for the implications of the operation on three fronts. This included the separation of the target militant groups, to get support from the political parties and to save the civilians from the backlash of the operation.