Mmm... I still think "Murphy's Brewery, Cork" would be better. (That would still group breweries by brewer by the way, and we can edit them to sort whatever way anyway though).
I feel like "Guinness, St James's Gate Brewery" only makes sense because it does be known as "St James's Gate Brewery"... Murphy's doesn't be known as "Cork Brewery" so that comma feels out of place.
Where as I feel the format of simply "[name] Brewery, [place]" works for either and any. What's the Brewery called? "Guinness Brewery", "Murphy's Brewery", "Smithwick's Brewery", "Wicklow Brewery". Where is it? "St James Gate", "Cork", "Kilkenny", "Redcross". So then "Guinness Brewery, St James's Gate", "Murphy's Brewery, Cork", "Smithwick's Brewery, Kilkenny", "Wicklow Brewery, Redcross"... (for example "Wicklow, Redcross Brewery" makes even less sense than it does for Murphy's and Smithwick's).
My two cents anyway.