The situation involving the Khmer Rouge is quite complex. They were initially associated with the "Communist" block, but closer to the Chinese side. So after the Soviet/Chinese split, they ended up opposite from the Vietnamese, who where aligned with the Soviet Union. That in turn led to the US supporting them when they went to war with Vietnam. The genocide was pretty much over at that point, since the Khmer Rouge had been in power for a while (those they wanted dead had already been killed) and lost control over most of Cambodia to the Vietnamese.
It was definitely a moral failure on the US side to support a known genocidal group based on "the enemy of my enemy is my friend"-type reasoning, but I don't think you can hold the US directly responsible for the victims that were already dead at the time.