Everybody's always a civilian when the enemy is about to take over the land. That's how it has always been in the region. Nobody puts on uniforms and openly admits to being a supporter of the enemy, much less an enemy combatant. Unfortunately this practice of intentionally exploiting civilian identity makes everybody a suspect. That's not new to this combat, it's a pervasive feature of all combat in the region, and has been for decades. Disgusting, yes, but not new.
What people find 'acceptable' hardly matters since this maelstrom of battling zealots has no common ground that is mutually acceptable. Partition of Jihadistan is already de facto, thanks to ISIS, and whether it's made de jure or not probably has little significance. The best possible outcome that could be hoped for is that Jihadistan is nominally made part of Iraq and Syria again, even though on the ground it will remain even more autonomous, and zealot-filled, than equivalent regions in Pakistan and Afghanistan. It is also going to be starved of the tax base and economic prosperity of the national centers. That's just reality. National unity is dead, dead, and shall I repeat myself, dead. As you say, the days of imperial dominance are over. But for that exact reason, partition is here to stay, like it or not.