I've heard this argument applied to guns, and I'm not sure it works. You can use a knife to cook dinner or to kill someone. The killing is misuse of the knife. Using a gun to kill isn't misuse, it's the intended use. The gun was made in order to kill. You can certainly have one as a novelty, but it doesn't change what it was designed for.
Yes, people have the free will to not follow Religion, just like they have the free will to not use a gun, but that choice to not use the gun doesn't stop it from being a weapon made to kill. Choosing not to partake in Religion doesn't stop it from being the tool it is.