I had the exact opposite interpretation of that line. I thought it meant that Harry still had so little control that if he was trying to get rid of a memory which involved the colour blue (presumably referring to the unicorn and its blood, which was "not white, but pale blue, or appearing so"), he would instead end up removing all such memories without meaning to.

That's rather like saying "he couldn't perform surgery unless he wanted somebody to lose every single organ in their abdomen". Not something you want to use as a tool - at most, it's a very blunt weapon where Harry has access to far better ones for most situations.