They weren’t morons, they didn’t have germ theory but they knew how disease worked:

Las Casas, Historia de las Indias: He was on Hispaniola during the 1518–1519 smallpox outbreak. “In December 1518 or January 1519 a disease identified as smallpox appeared among the Indians of Santo Domingo, brought, said Las Casas, from Castile. It touched few Spaniards, and none of them died, but it devastated the Indians.”

Read that sentence carefully. Las Casas, an eyewitness, in 1518, recorded three things: the disease came from Spain, the Spanish were largely unaffected, the Indigenous population was devastated.

On biological warfare, the Incan empire was destroyed and thrown into civil war by smallpox in 1528, and pizzaro showed up in 1532 to mop up the ruins. He didn’t cause the outbreak but he understood what was happening just fine and took advantage of it. He probably wouldn’t have been able to win without the diseases and he knew it