。
She was deeply loved by him.
Literal
She [topic-は] he [by-に] greatly was-being-loved.
A passive sentence: 愛される is the passive of 愛する, with に marking the agent ('by him'). Combining the passive with ~ていた gives a sense of duration — an ongoing state of having been loved over time. Where English often settles for a simple 'was loved,' Japanese reaches for ~ていた to underline the continuing nature of the relationship.