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I don't think they'd assume Eleanor was named after Suellen. But I would maybe have an Eleanor namesake in mind and preemptively mention it so that association doesn't have time to come into anyone's mind in the first place. (say "I really liked this name and I was also thinking of [any historical Eleanor(s) that make a good namesake]" when you first introduce the idea of naming your baby Eleanor).

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But that said, I don't even know the names of any of my friends' grandmothers, much less a random estranged step-grandmother. Your family already knows you wouldn't have a baby after Suellen and other people probably don't even know of Suellen's existence.