[PvK]

One reason to keep natives alive would be trade. If their production is inferior to yours, they can still receive trade income from full empires, which generates resources which wouldn't exist if they were wiped out. Players can then try to jip them out of those resources through diplomatic trade, threats, intel, or gift them ships which they could maintain on their trade income (unless the AI is too pathetic to realize it could maintanin them with low production but high trade).

Unique intel and techs would be other reasons.

Of course, it'll still be tempting to conquer them and use their population.

PvK