I think the movie rights were definitely still an issue when you look at how little mass media promotion Wanda was getting compared to other characters at the time, especially before the Fox deal. Even to the point that they altered promotional material for Civil War to not show her in it.
Future seasons of Assemble made sure to include every other MCU Avenger or hero aside from Wanda (and War Machine). When Vision shows up and becomes a main cast member alongside Wasp, who hadn't even actually done anything in the MCU by the time they used her in the cartoons, I think it's pretty clear they were deliberately excluding Scarlet Witch.