。
She thought of him as the one who had saved her life.
Literal
She [topic-は] him [object-を] life [genitive-の] benefactor [as-だと] was-thinking.
命の恩人 ('benefactor of one's life') is a set phrase for someone who saved your life — used both literally (rescued you from danger) and figuratively (pulled you out of a crisis). The structure ~を~だと思う marks the subject of thought with を and quotes the predicate with だと (copula だ + quotative と). The continuous past ~ていた ('was thinking, had been thinking') signals this was her settled view over time, not a momentary thought — and often, in narrative, foreshadows that the view later changed.