I think the most disturbing scene for me was Elena's monster transformation when she's in the courtyard looking out the window. I didn't see it until I got all the endings and started looking for all the scenes for the 100% completion. I didn't mind Elena eating beast flesh, I ate more gross stuff than that :P
When she does it when he's nearly fully transformed it's creepy. The way she does it, is that she yanks the flesh out of Aeron's hand and takes a forceful bite out of it and then smiles... Well, I guess it makes sense, seeing as how she knows she needs to in order to NOT be a monster.