I wonder if it's not a matter of how one uses the intense emotional energy with which Pluto infuses those with Scorpio sun signs? If a Scorpio's habitual methods of using energy include destructive patterns of jealousy, vindictiveness, revenge, and rage, then yes, control freak is one of the negative manifestations of lower-level Pluto energy. If, however, a Scorpio sun-sign person has been fortunate enough and dedicated enough to mature his/her spirit during this life, the "higher" qualities of the sign will manifest more often, such as service to others--perhaps instead of being a control freak, the "evolved" Scorpio will be able to practice great self-control when needed.
I think that continuing to uplift one's energy to one's Higher Power, be it God or whatever one respects in that position, will help "let go of that controlling nature" by directing the Scorpio's intense passion towards his/her highest love. Often, that must go hand in hand with self-work, removing ego blockages, negative patterns of thought, et al.