。
She loved him all the more because he had flaws.
Literal
She [topic-は] he [subject-が] flaws [object-を] is-having [because-ので] [on the contrary-かえって] he [object-を] loved.
かえって ('on the contrary, all the more') marks an outcome that runs counter to expectation — the flaws should logically reduce affection, but instead they amplify it. ~ので gives a softer, less pointed reason than ~から, which suits the slightly reflective tone here.