彼女が(かのじょが)汚れて(よごれて)いるのではないかという、都会的(とかいてき)な醜い(みにくい)「偏見(へんけん)」を抱いて(いだいて)いたこと

At first, I held a cynical, urban 'prejudice' that Kaoru might have been defiled by adult men, and fretted alone. However, one morning, seeing Kaoru waving her hands innocently stark naked from a riverside public bath, I realized she was still a complete child and an innocent being, feeling ashamed of the dirtiness in my own mind.