Well if you do allow light to cancel the darkness it basically creates 2 possible scenarios
1) Sphere of darkness is absolutely useless because it takes the dragons entire turn to cast, but the wizard can cancel it with a minor action. Using this power actually hurts the dragon because he's given up his entire turn for no effect.
2) The party has no wizard so sphere of darkness is still extremely powerful.
Ultimately I think it's silly to make the black dragon's color defining ability useless to the point that he's actually punished for using it. Allowing a second sphere to override the first light is irrelevent because the dragon is punished for the second sphere just as badly as the first one.
1) Sphere of darkness is absolutely useless because it takes the dragons entire turn to cast, but the wizard can cancel it with a minor action. Using this power actually hurts the dragon because he's given up his entire turn for no effect.
2) The party has no wizard so sphere of darkness is still extremely powerful.
Ultimately I think it's silly to make the black dragon's color defining ability useless to the point that he's actually punished for using it. Allowing a second sphere to override the first light is irrelevent because the dragon is punished for the second sphere just as badly as the first one.