i think the historical context for how the conflict with the spanish starts should be established. This is because in OTL the spanish had only sent 168 soldiers to "conquer" the incas. The majority of the troops supporting the spanish were the ones that wanted to see the inca gone/were siding with huascar and wanted to see atahualpa being brought to justice for the actual horrible things he did like the cañari genocide and desecrating the ancient tradition of taking care of the incan mummies as if they were still alive.
so if we atahualpa takes out the main pushing force that made the locals and spanish join together afterwards and form the viceroyalty of peru, because right it's called viceroyalty since the place was seen as an allied kingdom. But well, without these folk, would have the spanish even gone to war with the Inca or anything in the first place? Seeing that Atahualpa wins in your scenario, would there still be deep down groups of people under the incas (as OTL were the chachapoyas, wankas, chankas) that would be willing to create an uprising for the sake of turning over the inca and how less successful would it be with how much stronger atahualpa's side is now?