AI have used red wine in ganache but not BC. I think making a red wine ganache for a filling would be yummy! You could even brush the cupcake with the red wine (like a simple syrup) either or both would be yummy! I have infused several several types of liquor into BC though and I've never had a problem.
I have done it with champagne, but not red wine. I would try just a little, and see how it tastes. I would definitely reduce it first, maybe just a quarter cup, then mix that into a small amount of the butter cream and see how it is.
If it's no good, you will only have wasted 1/4 cup.
For a filling I would probably play with the flavours in the wine. Red wines often have blackberry or cherry notes, so maybe a blackberry compote inside? (or whatever fruit/berry matches)
AI just goggled a couple recipes for the red wine smbc and they do reduce the wine to a syrup, with a little sugar.
http://www.mission-food.com/2012/05/chocolate-cupcakes-with-red-wine.html
http://thecupcakearchitect.blogspot.com/2012/09/chocolate-red-wine-cake-with-red-wine.html
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