And thus would have the right to kill those holding such beliefs?
It's mot matter of judging actions of long ago by today's standards. Stephen was murdered for his beliefs stated before the Sanhedrin. They too might argue they had a duty to stop this heresy but then as now these men were murderers and those who, like Saul, approved were just as guilty.
“Further the Catholic Church has also always viewed itself as the “Body of Christ” and Christ did instruct His followers to take up the sword to defend themselves”
Not so. When the disciples showed up with two swords Jesus said “that's enough”, and rebuked Peter for using a sword on the High Priests’ slave since Jesus could call on legions of angels for protection.
Where were swords defending James or Stephen, Peter, Paul?
“The Catholic Church has maintained that we hold the fullness of faith and that inherent in that is a duty to protect others from falling into heresy.”
The Pharisees had the same view and were willing to murder anyone who disagreed, even the resurrected Lazarus, lest the Romans come and take away their positions and nation.
You are certainly free to agree or disagree.