I've heard it said that the costume actually makes professional sense. Putting Deanna in an outfit where her rank isn't thrust in the face of her patients. If they were contstantly being reminded (by the uniform and rank pips) that they're being asked to 'fess to a woman who is their Commander as well as their counsellor, a junior officer might be less willing to go to her with their troubles.
Personally, there's a part of me that kinda wishes they hadn't given her officer rank and put her in a uniform in the pilot episode in the first place. That
was the mistake, if anything. The character might have been better served if the implication was of her being essentially an outside civilian in a high position. Of course, it would be hard to accentuate
her importance in the ship's hierarchy without showing her rank...