The Jews began persecuting Jesus' followers because Stephen had said and done things that the Jews did not like. Because of this persecution, many of Jesus' followers left Jerusalem and went to many different places.
# those ... spread
"those went in many different directions"
# who had been scattered by the persecution
This can be translated in active form. AT: "whom the Jews had been persecuting and so had left Jerusalem" (See: [[:en:ta:vol2:translate:figs-activepassive]])
# the persecution that arose over Stephen
the persecution that happened because of what Stephen had said and done