I suppose I could switch the upper and lower floors, putting the bees on the top. Only problem with that would be the loss of space. I don't think that I can fit a brewery and owner's lodgings in the same space as the main floor. Would it be acceptable to have cold marble floors for the areas related to storage and brewing or would that seem "too convenient".

Oooo or I could separate the brewery from the actual tavern, i.e. a separate tree with holey floors for ventilation. I can't say that I know many things about bars or taverns. I appreciate the pointers though.