I have seen quite a few comments saying things along the lines of 'she's not black why does it matter', and 'i doubt Japanese people had a problem with this'.
You are right, she isn't black however colorism is prevalent throughout Asia (including Japan), and the conversation surrounding colorism and its consequences is getting louder and louder each year. I have no doubt it left a sour taste in many Japanese reader's mouths when she became 'less dark' and suddenly was accepted by society. Does this make sense for the plot? Yes, absolutely, however many Asian people (including Japanese people) bleach their skin in order to become lighter and in turn be more accepted by society. I'm sure for many readers it felt like a reflection of their lives, where they were told that in order to be more successful, pretty, or attractive they had to become lighter.
Colorism is a thing, look it up before you make assumptions. Clearly, the publishers realized what a bad message changing her skin sent and changed it afterward.