Where I quote from it, I do so in red. As you point out, not all suffering is without a good side. Some pains warn us about other, greater pain. This is a good indication that we have been designed by natural selection and not by an all-powerful God. This sort of pain is just what we would expect from natural selection, which is a jerry-builder.
People get pains from phantom limbs.
Many very serious cancers develop without any initial warning pain. Christian doctrine is that resurrected bodies will be material, physical bodies , able to be touched. So your statement is bad news for people who think there will no longer be pain when they are resurrected. The Gospels state that the resurrected, material body of Jesus still had wounds which could be touched , yet presumably Jesus was not in pain and not suffering. However, I don't see why this is a problem for atheists.