***Not a teacher***
To say 'had already been taken care of' identifies this as an event that was completed in the past (but which has an effect in the present).The liquor licence was already taken care of and the premises, an old gambling club, had been given a lick of gold paint and new brocade curtains.
To say 'was already taken care of' places an emphasis on the ongoing effect in the present (with the implication that it was completed in the past).
So I think it is just a matter of emphasis - whether it is the completed nature of the event, or whether it is ongoing nature of the effect in the present.
In the context you gave, I would slightly favour 'had already been taken care of', but in my opinion, both are acceptable.