Who was it that sanctioned the inquisitions for 686 years? Answer, 99 popes of the Roman Church. The apostles overruled the scriptures concerning circumcision of their own accord at the first ecumenical council. Did they have the authority to do so?
Based on your premise that apostles overruled the scriptures, Rome]s so-called successors could claim they have the authority to do the same as regards the use of the sword of men in order to enforce theological conformity.
However, the apostles and elders and early church (together) did not such overruling of scripture (which is nigh to a blasphemous charge!), but instead they acted in accordance with scripture, which promised a new covenant. (Jer. 31:31-34) Under which manifest grace, in contrast to salvation under the Law "To him give all the prophets witness, that through his name whosoever believeth in him shall receive remission of sins," (Acts 10:43) And God, which knoweth the hearts, bare them witness, giving them the Holy Ghost, even as he did unto us; And put no difference between us and them, purifying their hearts by faith. (Acts 15:8-9)
Thus seeing as Scripture promised a new covenant, and manifested to the disciples of Christ that they were under it, treating Gentiles just as circumscribed believing Jews, then they could hardly be acting consistent with Scripture in requiring born again members of Christ to be circumscribed and keep the law (which was what the issue was, as circumcision represented this).
Thus Peter's response, "Forasmuch then as God gave them the like gift as he did unto us, who believed on the Lord Jesus Christ; what was I, that I could withstand God?" (Acts 11:17)
Now therefore why tempt ye God, to put a yoke upon the neck of the disciples, which neither our fathers nor we were able to bear? But we believe that through the grace of the Lord Jesus Christ we shall be saved, even as they. (Acts 15:10-11)
Then James issued the final judgment, substantiating it by Scripture, invoking prophecy of what God would do in the latter days, and proposing what to do, to which all concurred.
Thus rather than overruling Scripture, Scripture overruled the Judaizers as the NT overruled the Old, as it said it would, being distinctively "Not according to the covenant that I made with their fathers in the day that I took them by the hand to bring them out of the land of Egypt; which my covenant they brake, although I was an husband unto them, saith the Lord: (Jeremiah 31:32)
However, the men such as the apostles could speak and write as wholly inspired of God at times, and also provide new public revelation thereby, neither of which even Rome's leadership claims to do.