I have thought about having ground troops be able to attempt to kill off a population. This isn't as straightforward as it sounds though. Firstly, the population might resist and form some type of poorly-armed militia, although based on Earth history this isn't necessarily certain. Secondly, it would be a huge undertaking. The Holocaust is the prime example of an industrialized society attempting to do this. Putting aside for a moment the abhorrent nature of the attempt and looking at the logistics, the ####s apparently believed that their own troops would simply not be capable of simply shooting so many people, for both logistical reasons and because of the psychological effect on those troops. Eventually they turned to what was really industrialized genocide, rather than military-led genocide. Also, even though the holocaust is generally regarded as the worst crime in human history and killing six million people is almost unimaginable, that is only a tiny fraction of an entire planetary population. Can you imagine trying to wipe out six billion people and keep it a secret to avoid massive resistance?
If you really wanted to kill the population then you really need WMD, which means nuclear, biological or chemical. In this case nuclear means collateral damage, chemical is probably the terraforming option and biological isn't in the game yet, although it will be at some point. In summary, getting your troops to simply kill everyone is probably the most difficult option and I doubt it could be done in reality.
Steve