Changing the legend names
You don't have any continuous fill scales, since you're filling according to Condition, which is a factor. This is leading to the Error: Discrete value supplied to continuous scale error. You just need to combine your previous scale_fill_manual(values=...) command with the labels= part of your incorrect scale_fill_continuous() command:

ggplot(dataset, aes( x = Norm, fill = Condition, y=log2(measure))) +
    geom_boxplot() +
    scale_fill_manual(values=c("brown1","darkolivegreen4","burlywood3"),
                      labels = paste("condition1", "condition2", "condition3")) +
    theme_classic() + 
    labs(title="Comparison",x="Norm", y = "counts")


Something along those lines should work.