I think the scene that you're referring to does go with The Family of Blood episode where The Doctor was dealing out the punishments.

I think the specific punishment was for the Mother but I don't think it was a black hole... I think it was an "event horizon of a collapsing galaxy." I checked on Youtube for that clip.

I wouldn't be surprised if The Doctor still has The Master's black hole device... could come in handy in the future? ^_^