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I had assumed she would naturally come to our wedding.
Literal
She [topic-は] naturally our wedding [to-に] come thing [quotative-と] was-thinking.
~ものと思っていた expresses a past assumption or expectation that was held over time — 'I had been thinking/assuming that...' 当然 ('naturally / of course') strengthens the assumption: the speaker took her attendance as a given. The past progressive 思っていた (rather than 思った) emphasizes the duration of the belief, making it clear this was an ongoing assumption, not a momentary thought.