Starting in version 2.0.0 of ggplot2, there is an argument to control point border thickness. From the NEWS.md file:
geom_point() gains a stroke aesthetic which controls the border width of shapes 21-25 (#1133, @SeySayux). size and stroke are additive so a point with size = 5 and stroke = 5 will have a diameter of 10mm. (#1142)
Thus, the correct solution to this is now:
df <- data.frame(id=runif(12), x=1:12, y=runif(12))
ggplot(df, aes(x=x, y=y)) +
geom_point(aes(fill=id, size=id), colour="black", shape=21, stroke = 2)
