Genocide on planetary scale is trivial in context of the galactic civilisation. It's less significant on galactic scale than the bombing of nagasaki or dresden on earth scale. Especially as planetary scale in the galaxy far far away is often less than the population of either of those cities. And the scale of those attacks was rather limited, the war would have been a total different one if it would have been a war of extermination. And the separatist senate would never have accept such a war in the first place, the war crimes had to be small enough to hide it from their own senate and population.
5 Million clone troopers was considered a large number for the war efforts, so indeed, a proxy war which only small investments.
Edited by SEApocalypse