In my dissertation work, I'm attempting to develop ethical guidelines for when non-state groups have the right to go to war (that is, when they have Right Authority). My claim is that non-state groups can often represent their communities as well or better than state governments can, and the current argument that only states are allowed to go to war is absurd.
At the moment, my current obstacle has to do with one of the traditional requirements for Right Authority: the Authority's ability to control and discipline its subordinates. Basically, if fighters on your side are running rampant, attacking civilians, disregarding your orders, and ignoring attempts to broker ceasefires with the other side, then there is a serious problem with your claim of being a Right Authority. That's the way that the issue is presented, anyway. Underlying this treatment is the assumption that armed groups are part of a hierarchical chain of command.
The problem is that when you look at conflicts like the Mindanao struggle in the Philippines, many armed men are part of mostly-autonomous bands that might affiliate with MILF one day, with Abu Sayyaf the next, and pop off for a spot of independent banditry on Sundays. While they are certainly influenced by the demands of the organized group leaders, to call them part of a stable chain of command is ludicrous. Yet, given that, should the existence of such groups harm the standing of the organized units like MILF? That is, should you view such groups as examples of a failure of MILF discipline? Or should they be viewed in another way altogether, one that better fits the facts of the case?
Right now, I'm leaning toward the latter view. I think the best way to look at such groups is as members of an alliance with the major armed organizations. And that brings us to a key point: while political theorists have wrangled back and forth over the ethics of warfare, there has been practically zero discussion that I can find of the ethics of wartime alliances. Can you ally with bad actors? What obligations to control them might you have? If you do ally with bad actors and then fail to control them from committing atrocities or the like, does that ethical breach stand on its own or does it harm your own standing as a Right Authority?
I don't know the answer yet (though I suspect I'll be doing a lot more reading about civil wars, such as this book that comes highly recommended by some big names in the field). But I find it encouraging as a budding young scholar to discover such a rich vein of apparently untapped questions—especially since the topic of ethical alliances could have applications ranging from international relations, to civil wars, to even the institutional workings of democracy itself.