I don't think he was killing the Manichees PRIOR to his conversion.
I didn't realize Justinian converted! Christianity was well established by the time he was born and it was a state religion, so I would imagine that he was baptized shortly after birth.
Eastern sainthood is attained by spontaneous popular veneration. Many kings were sainted for what they have done for the Church. Heads of state are not held directly responsible for lawful (not necessarily "just") killings committed by the state. I am not sure that Justinian personally killed anyone.
You are making a strawman.