The logic here is that people tend to associate "red" with "enemy." Things on the map are coded by team color because they don't move-- you know who owns what because of its location, and that will never change. (Though I wouldn't be opposed to "your" structures always being blue.) If scoreboard values were colored the same way, then you'd run into issues with people having difficulty determining which is theirs. If half your games have the scoreboard colors reversed, it'll be exceedingly confusing.
I could see this maybe working if Blue scores were always on the left, and Red on the right-- keeping Friendly on the left but changing the colors would be needlessly confusing.