Is it possible to use the stroke argument introduced with ggplot2 2.0 to adjust the thickness of borders around bars? If not, is there a way to control bar-border
ggplot2 2.0
well as I suggested by the OP, I will just recopy my comment as an answer.
you just need to set size in your geom_bar() expression:
size
geom_bar()
geom_bar(stat = "identity", aes(fill = "transparent", size = ifelse(factor2 == "A", 2, 1)), size=2)