Twilight Commander organiser and probably be able to use some form of artillery spell
Pinkie would probably be weapons expert, although her pinkie sense will come in handy on the front line
Fluttershy while it breaks character slightly i can see her providing animals for the war effort like some armoured bears or possibly be the person torturing POW for infomation with this
Rainbow could work as both messenger and Air force given her speed
Rarity could work in Army kit maybe designing camo gear
Applejack would probably be frontline