Every so often, some genius of strategy suggests using bullets dipped in pig fat to scare Islamic opponents. If history is any indication, deliberate or even accidental insensitivity to the religious views of others is a recipe for trouble. For example, Enfield rifle cartridges as the proximate cause of the Indian Mutiny. As for scaring the foes by threatening to bury them in pig skins, that impressed them no differently than the threat to piss on the American flag would impress you. Rage, not fear is the likely result.
The other purpose of desecrating the enemy living or dead is improving the morale of your own troops. But some of our troops and many of our allies are Muslim, even if belonging to other sects. So the practice is extremely counterproductive.
The key to effective warring against religious crazies is to ignore their religion. The British made no effort to counter-preach against the Mahdi. They simply wiped out his men with cannon and machine guns for the same reasons they had killed other hostile tribesmen: to establish control of a territory and to avenge the earlier deaths of British soldiers. Religion had nothing to do with it, and the war certainly wasn’t acknowledged as a conflict of faiths. It was a conflict of modern against the primitive and presented as such with no apologies. Similarly, in the suppression of the Boxer rebellion, the mystical aspects of the uprising were ignored and the believers in their own bulletproof nature were shot dead with efficiency.
So I would recommend limiting the reasons for warring on the people who may be Muslim to the same reasons used for warring on atheists or people of other faiths: murder, kidnapping and the like. Validating other people’s claim that America is warring on Islam in general is not just unhelpful, it actually does the enemy’s recruiting for them.