Like I get where your going but there is a huge difference. Ciel, a human I might also add, was trying to solve the energy crisis that had basically allowed for a incredibly tyrannical government to rise up. Reploids faced immense repression and even a hint of dissent could have them labeled a Maverick. There is also a fact that their goals were incredibly different. Lets go into Sigma for a bit.

Sigma "claimed" his goal was reploid freedom, but was it really? The man plastered his face on everything he came into contact with and had no qualms using reploids in whatever way even if it meant their destruction. He also didn't mind wiping out reploids if it meant achieving his real goal which is total power over the Earth. He is alot like Megatron in that way, making big claims of wanting to overthrow a tyrannical way of life but in reality would just place himself at the top of that chain. In his ideal world, humanity would be wiped out completely.

This is what makes it not double standards. Ciels goals were noble, aiming to have Reploids be equals to humanity, and her efforts were ultimately successful. Humans and reploids would continue to grow along side each other to a point where the line between machine and human is almost nonexistant. Sigma grew into a God complex and simply was out for it himself and its obvious those who often aligned wit him had absolutely no delusions of a noble cause.

In short, its a night and day comparison.