Everything is clear and more evident in hindsight. It seems that as far as Duncan knew, that pregnant woman was suffering from malaria, not ebola. She died while he was in transit or shortly after. He would not have had that knowledge.
"Knew", or very possibly hoped. She died in the house he was living in, and the end symptoms are sufficiently different that if you know which is which, you'd know. But we can't assume he would know to be able to do a differential diagnosis.
