The hammer makes it easier to understand that you can use it as an emergency weapon to hit people with.
Well if you give a flag an attack animation then anyone can put 1 and 2 together and realize that it can be used for attacking, or you could have the flag attached to your character's back so you can use other weapons and still hold the flag. Personally I don't think the flag holder should be able to attack anyways.
Although you could rename the gamemode "Capture The Hammer" because that makes more sense than Capture The Flag right now.