I think Peaceful Transfiguration should be more of an active ability rather than an automatic one. Weapons such as "mortal" guns and blades will be easier to transform into something harmless, while weapons of magical origin will require more effort. The transformation should also have a time limit related to how much willpower the guy can exert into keeping it that way. Again, normal weapons will be easier kept transformed, while magical weapons will require more effort to keep in their harmless form.

As for the flex thing, if you really want to keep it, it should be more of a soothing aura thing whose more potent form can be activated for a certain period of time.

These are my suggestions.