Atahualpa had a plan to capture the Spaniards and killed them all but three (aside from keeping the horses); the blacksmith, the gunner, and the barber.
The first two for obvious reasons, and the barber beacuse he had the "power to rejuvenate men" after shaving them

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In any case after the end of the civil war the Incas were in no position to go conquering anywhere; the demographic collapse suffered by both the epidemics and the war itself at caused serious labor and military manpower shortages which would not have allowed the Empire to run as efficiently as it would have in the pre-1525 period. Expansion in any direction would be out of the question, to consider otherwise would be ASB. Ecuador itself had only been pacified by c. 1523 (hence all of the professional armies being in the north.)
Unless European contact can be delayed by at least a generation, or Wayna Qapaq survives the plague, eliminating the civil war, there really is no chance for survival for the old Empire.