This is very common in households with two intact bitches unfortunately. It's why a lot of the time people in the basenji breed recommend opposite sex parings for pet homes. I know of several people who have to constantly rotate dogs that don't get along. I know that's not something I could do because of the size of my house and the stress it would put both me and the dogs though. Spaying them might help since the issues started with the rottie's heat cycle. You didn't mention if the basenji was still intact or not.
Hiring an in home trainer could help. They would be able to see the dogs in their own environment and figure out a way to keep them both safe.
I know you don't want to do this but it might be in the best interest of your girls to re-home one of them. Like you said, your rottie is trying to defend herself and could easily hurt your basenji due to her size. I had a friend who had to make this decision and it was hard on her and her family but it was the right one for both dogs. Her small terrier was so aggressive towards her massive Irish wolfhound he was afraid to go outside. Re-homing the terrier made both of them happy.. he has a family where he can be top dog and the wolfhound feels safe again. It's not an easy decision.
Do you have family that could take your rottie girl? Try a trial sepperation and see how it goes?