I hope that you and your sister will one day reconcile. I understand why you had to distance yourself from her and if I were you I'd do the same. I haven't encountered what you are dealing with personally but I have seen the color scheme play out in my best friend's family and, like your sister, I have had conflicting feelings about color and race.
For my best friend, she and her siblings are biracial (although they didn't know their dad). My bf could pass for latina or white at times but she's a proud black woman. She has a sister that isn't biracial and is fully black and by black I mean dark. They look like one another except a positive and negative photo. Because she is dark my friend's mother (who is black) favored her. She felt she would have a harder time in life because her skin is so dark. Because of the favoritism there is a strained relationship between the two sisters, but not because of my friend but the sister. Once I ran into the sister and said hi, she asked me how I knew her and I told her I was a friend of her sisters. She told me she had no sister. My friend still loves her older sister and says she understands why her mother played favorites (she died years ago) but still feels a bit hurt by it.
I also have conflicting feelings about race. I have a monoracial dd and a biracial dss. They are both in their teens and get along well. I think if dss was a girl and/or they were pre-teens or younger things there would be a different dynamic between them but as it stands now my dd is fiercely protective of dss although they don't interact a lot because of the age four year age difference (my daughter think dss is a baby; dss thinks dd is a nerdy girl). My conflicting feelings about race come in as I think about having children; can I see myself holding a lighter baby? How will I feel if the child doesn't look like me --or worse yet if the child does? Will I be secretly happy that my genes won out over my husbands or saddened that I don't have a kid that looks like him? And for someone who is dark skinned like myself, it has been a hard fought road to own my own beauty, especially since society is eurocentric. And I have to admit I am glad that there will be a big age difference between my dd and any prospective kids that dh and myself will have because I don't want the world coming in between the sibs & I think it will be easier for my dd to have what ppl (esp those in the black community) will deem as a cute baby as a little sister or brother when she won't be in direct competition for attention.
Hopefully this is not TMI. But back to your sister....
The worst thing your sister can do is treat the darker ones differently because they will soon pick up on why she's doing it and feel second rate instead of equal to your kids. She thinks she's going against the grain but instead she's playing directly into the notion of lighter is better by treating the kids differently. Hopefully you and your sister will get a chance to have a long and in depth talk to hash these things out sometime in the future. She sounds hurt and insecure and doesn't seem to have reached the conclusion that you have: that black is beautiful no matter what shade it comes in.