If you figure out a vector of colors for your facets ahead of time you can hack it like this:
library(ggplot2)
library(grid)
df = data.frame(a = rnorm(100), b = letters[1:2])
ggplot(df, aes(x = a)) + geom_density() + facet_grid(.~b) + theme(strip.text.y = element_text(color = c("black", "red")))
mapply(
function(g, co)grid.edit(g$name, gp=gpar(fill=co)),
grid.gget(gPath("strip.background"),grep=T),
c("#F8766D", "#00BA38")
)
#R 3.1.0 ggplot2_0.9.3.1 on Win7 64