I'm surprised no one has mentioned any of the America's Army series of games, where if you kill an injured opponent you face a major penalty(I only read about it, so I'm not sure what it is).
When it comes to fighting off alien invasions, the IHL and IHRL both rightly get thrown out the window, as they are not humans. Of course, it would probably be a good idea to preserve important social landmarks, as doing so and still being able to win would represent major moral victories.
As mentioned above by at least DeanoTheGod mercenaries and non-state militias do not have to abide by the IHL and IHRL. This makes for a major twist when using asymmetrical warfare.
I can't really take anything like this seriously because several things that are considered war crimes, i.e. the killing of incapacitated enemy soldiers, are just common sense, and I doubt that there is a major military commander on the planet who tells his or her soldiers to risk their lives to preserve the lives of their enemies. After all, you can't tell who is incapacitated or who is faking until you get close enough for them to kill you. Get some war crime laws that make sense in the context of war and I can listen, but until that happens I think it's ridiculous for them to be moralizing.
With the Resistance example, I think the fact that they are fighting evil alien/mutants/whatever I'm not up to date should outweigh the fact that they are fighting in a church.