So I have a data frame in R called obesity_map which basically gives me the state, county, and obesity rate per county. It looks more or less like this:
obesi
I think all you needed to do was reorder the map.county variable like you had for the map.data variable previously.
....
map.county <- merge(county.obesity, map.county, all=TRUE)
## reorder the map before plotting
map.county <- map.county[order(map.data$county),]
## plot
ggplot(map.county, aes(x = long, y = lat, group=group, fill=as.factor(value))) + geom_polygon(colour = "white", size = 0.1)