In that article I see no indication that the "internal investigation" is the ONLY thing happening. It says nothing about whether the case was referred to the DA, nor does it indicate if charges have been dropped.
Sounds to me like this guy will possibly lose his job in addition to criminal penalties.
For the life of me I can't remember the PC section for brandishing, and my search skills are tired and a bit hung over... so I'm not certain, but I think brandishing is a misdemeanor. LEOs aren't allowed to arrest for misdemeanors unless it occurs in their presence; otherwise, they issue you a citation and release you. (There is an exception if they can't positively ID a criminal suspect.)