Imho, the eclipse was revolting. It made me angry and disgusted, and although it's also unsettling, those feelings aren't as disturbing as Ganishka's form to me. Why?
Disturbing usually refers to something that shouldn't be there. The rape is a human thing, it felt common place knowing Griffith's feelings and Caska's feelings. Not that it wasn't very violent, it was! But it's something we can understand and reason with. It's part of our world, and Guts' suffering actually exists in a war-like scenario. Several people undergo that much anger and violence in the real world: it's bad but it's not Escher.
If I were to pick the disturbing parts of the Eclipse, those would be the demons eating the Hawks. The Count specially, since he did appear in there as well, and ate the Hawks as well. It was really unsettling to see creatures that came out of nowhere and that we couldn't make out were their mouths were. Fairies too, it makes no sense to see a fairy or a God-hand for that matter.
Ganishka was to me the very description of disturbing, since one doesn't understand where is his face and what are those things around him. Something quite that huge is trully disturbing to see, it's nightmarish and not of our world, and that would happen by its size alone. His "octopusses" are as 'weird' as many of the apostles seen on the Eclipse, and his whole body reminds us of that scenario. That's the reason I pick Ganishka's form over the Eclipse. Imho, Miura took a step further in disturbing on that part than he did on the Eclipse, as the latter was still very human (we would get that same feeling from being chased by beasts in a dark forest, or by bandits in an alley).
Although I quite understand your views, I just felt like I had to justify (and perhaps give an opportunity to change some of the votes) my choice. The Eclipse is indeed quite a candidate, but I spent over 10 minutes looking at the computer when I saw Ganishka's first full body drawn. That concept really blown me away, there was a long time since I saw something beyond my own imagination capability. And I considered that one of those moments.