Closest match I've found so far is The Wind Singer by William Nicholson.
The book begins in the walled city of Aramanth, an extreme meritocracy where endless exams and ratings are the only way to move forward to improved life stations; to be unsuccessful in this is seen as a great source of shame. Using a system based on colour classifications, the governing Examiners dictate what people can wear, where they can live and what jobs they can do. The levels are grey, maroon, orange, scarlet and white, with the muddy Underlake the lowest and white the highest. The Emperor is the only person allowed to wear blue.
A minority in their society, the Haths believe more in ideas and dreams than in endless toil and ratings. When young Kestrel defies the harsh classification system of Aramanth she flees, finding herself in the company of the Emperor of Aramanth. Thought to be the ruler of the city, he is found to be merely a puppet of the High Examiner, and the Emperor tells Kestrel of the need to rid Aramanth of the influence of the evil Morah, of the need to return the voice to the mysterious Wind Singer that stands in the city arena.
Using an archaic map given to her by the Emperor she sets off, joined by her twin brother, Bowman, and their brave but pitiful new friend, Mumpo, who has an unshakeable affection for Kestrel. They meet a variety of tribes and individuals including the fearsome nomadic clans of Ombaraka and Omchaka. The journey eventually leads them to the Halls of the Morah; the very heart of the evil that has taken control of the city. Here the children finally retrieve the voice of the Wind Singer, in the process waking the terrible Zars, an army of the Morah. Pursued by the beautiful, evil and unstoppable Zars, the children race back to Aramanth, arriving just in time to return the Wind Singer's voice. The voice allows the Wind Singer to emit a powerful song that destroys the Zars and saves Aramanth.
Color-based society, female protagonist with a sibling, and it came out in 2000. However, red is not the lowest caste.