To be fair, a game that included (say) developing new forms of consciousness and levelling up the entire civilisation after contact with aliens would have been a bit harder to bring to market.
Well, Civilization included alternative ways of creating a dominating society: war, trade/diplomacy, technology. And this was in favor of fun! You had diversity in strategic decisions, you had to consider different approachs to a problem.
Yup. Quite a few sneak-em-ups and multiparadigm first-person games offer mostly- or wholly- pacifist routes through too - Thief, Deus Ex, Dishonored etc.