Among a single species, with a 50/50 split of a genetically diverse and homogeneous population, if you eliminate 10% of the former and 75% of the latter, the split becomes 80/20. If that distinction stemmed from genetic factors, you have selected for diversity.

Genetic diversity isn't only advantageous to the population. It's advantageous for the individuals that carry it, depending on the circumstances. Therefore it can easily be selected for.