I can't say anything bad about ONI. Literally <.<
I see why.
For the question: I think they're just disturbingly evil and have made the worst things anyone could do... well, excluding the things Faber has done of course. However, they do the things they did and do for the best of Humanity. For example, they keep on researching the Flood to develop the best tactics possible, despite it being very... inconsistent and that led to many outbreaks like the Mona Lisa.
I hate them, but they're extremely important in Halo's narrative and it wouldn't be the same without this disturbingly shady organization.