So I started running this campaign, and had four sessions so far. It is quite fun, but the atrocities of war show through quite a bit. Here are a few things that I am surprised about:
1. Desperate people are willing to do desperate/terrible things. Given the setting, the PCs had no issues committing acts of terrorism, just because a commanding officer told them to. In fact, they didn't even question it when they were told to destroy a lighthouse so that enemy trading and supply vessels would crash into a nearby reef.
2. Following orders is easy. Leading is hard. I gave my players an option to be the captain of a privateer vessel, but none of them wanted to be the leader, and deferred that responsibility to me without a second thought.
Just remember, people are pretty keen on doing evil things when they are disassociated from the final result. Even regular people today. If you want to toss in some moral quandaries, it might be necessary to hit a little "closer to home" as it were. Or for them to see the results of their efforts. Of course depending on your players and their characters, that still might not effect them very much. In that case WOOOOOH TEAM EVIL
A fine line. But there is a chance for redemption. Yes, the beginning can be bleak. Real bleak. But throughout you can introduce elements such as convincing attackers of Mercy. Maybe it's just really bad leadership and the goal is peaceful reconciliation. The invasion might not have been going too long, not many atrocities under their belts.