Not counting the PSP game or manga adaptions (neither which are fully handled by Gen), Sayaka and Homura have been shown to get along fine under different, potentially happier circumstances.
It would make for a nice revelation that deep down Homura admires Sayaka for her strong ideals and confidence, especially as they are used to protect Madoka, the person they both call their best friend. It wouldn't be a stretch to think that Sayaka is the person Homura wishes she could be, while the cold and detached personality she created was necessary to endure her own suffering.
