I suppose it's open to SOME interpretation, but I got it from this line:
"Our influence exists only because we sow accidents among the refugees, namely those who threaten the peace or otherwise prove detrimental to the administration"
"Even if it means condemning them to oppression and exploitation?"
"They will not remain outsiders forever"
That kind of sounds to me like what I was talking about.
Your interpretation seems correct to me, but I get the feeling this was kind of a retcon by the author. The other person was also correct that the people shown to be assassinated originally were both gang members, not refugee leaders. Of course, they had to start with that concept for anybody to be remotely sympathetic to the murderer main character, and I think they maybe lost sight of that when it came time to expand on the factional motivations...
At least, that's my impression. So far I've felt this is more like a "turn your brain off" spy flick than some kind of intricate, masterfully crafted plot.
But, on that note while my brain is on, the defense provided by 'Babylon' for not helping the refugee situation doesn't make any sense to me. They contend that the refugees should be accepted without using force -- and that's literally Babylon's schtick. We got treated to a whole monologue by her about how good they are at causing undetectable 'accidents'. If that's the case, it would be simple for them to remove a few powerful figures who stand as obstacles to refugee rights, without getting the refugees themselves embroiled in conflict or the use of force.
In the end, for me at least, I think this manga is more enjoyable if I don't think about it too much. Some things are just meant to be fun and entertaining on a surface level rather than deeply analysed.