Yes, it is wrong to pray for someone to die.  You are correct that the Ten Commandments state that thou shall not kill.  Not only should we not kill, but also we should strive to have love (agape) in our heart for all. Agape love is God’s love. It is not a soft feeling, nor a feeling of brotherly love. Agape is a decision to only do good to everyone. “…He (God) makes His sun rise on the evil and on the good, and sends rain on the just and on the unjust.” Matthew 5:45 NKJV

In the New Testament, Jesus says the commandments can be summed up with two rules, “Love the Lord your God with all your heart and with all your soul and with all your strength.  The second is this: Love your neighbor as yourself”, Matthew 12:30-31.  We are told by Jesus to “Love (Agape) your enemies and pray for those who persecute you,” Matthew 6:44.  This is very hard, especially when others are actually hurting you.

Christians face persecution because the darkness hates the light. “Yes, and all who desire to live godly in Christ Jesus will suffer persecution.” 2 Timothy 3:12.  However, if we obey the Lord and learn through our trials, we will grow more Christ-like. Then we will have a great reward. Romans 8:17, “…if children, then heirs–heirs of God and joint heirs with Christ, if indeed we suffer with Him, that we may also be glorified together.

God will certainly set things straight during Christ’s reign. “Beloved, never avenge yourselves, but leave it to the wrath of God; for it is written, ‘Vengeance is mine, I will repay, says the Lord.’” Romans 12:19.