From the versions of the story I have read, she was indeed upset over her change in colour and performed austerities to regain her prior form. It seemed strange to me, too. In thinking about it, I had a few ideas (about the actual story, that is - in Om Namah Shivay, she seems very upset about it in a vain way).
-Maybe she was upset simply because she had gotten used to looking a certain way and didn't want to change...and maybe her reaction serves to teach us about being too attached to form. When we get upset about appearances, we can remember Parvati-Kaushiki and know that appearance isn't that important, and also that great good can come out of events that initially seem bad.
-She might have been unhappy because dark or "black" complexion is associated with fierce goddesses like Kali. Maybe she thought her devotees would be afraid of her, or that she would be considered ferocious instead of benevolent.
-Shiv hints that she is dark because of some event to come. Maybe she was upset knowing that there was going to be violence and unhappiness in the world, since the dark colour would foreshadow a need for her to be fierce.
I hope other members have more ideas. The story confuses me, too.