The show has gone in a different direction with the humans under occupation. In prior seasons the cylons were in the middle of a debate about their own "humanity" and you could see the conflicts arising in their ranks about killing humans versus trying to be like them. Of course they eradicated 99.995% of the human race before coming to that point but that's a different matter.
There is a very clear Islamic analogue to that - this is the Islamic treatment of "dhimmis" who have submitted (or been forced to submit) to Islam. Even the "nice" cylons' approach was not "live and let live", it was submit to us because we know what's best for you, combined with a murderous religious fanaticism.
There aren't too many things they could do to be more clear about it, aside from calling the cylons' god "Allah".