Complex sentence: Variolation had the disadvantage that the agent used was in fact Smallpox, albeit the selected less lethal form (Variola Minor) and that the disease could either kill the inoculee or spread in its full form to others nearby.
Split into simpler sentences: Variolation had the disadvantage that the agent used was a less lethal form (Vaiola Minor) of Smallpox itself. Hence it could kill the inoculee or spread in its full form to others nearby.