How are Christians to resolve disputed issues?

One of the protestant traditions, first articulated by Martin Luther, holds to this day that the final authority is the Bible for resolving issues of doctrine. From the bible they usually support this position with “All scripture, inspired of God, is profitable to teach, to reprove, to correct, to instruct in justice” (2 Tim 3:16). It usually fails to convert those who hold to this error by pointing out that the scriptures spoken of here are what we know as the Old Testament only, or that Holy Scripture itself says “...the house of God, which is the church of the living God, the pillar and ground of the truth” (1 Tim 3:15), and even though Jesus said that the way to resolve an issue is to take it to the Church: “But if thy brother shall offend against thee, go, and rebuke him between thee and him alone. If he shall hear thee, thou shalt gain thy brother. And if he will not hear thee, take with thee one or two more: that in the mouth of two or three witnesses every word may stand. And if he will not hear them: tell the church. And if he will not hear the church, let him be to thee as the heathen and publican” (Mt-18:15-17).

Here is an additional argument I haven't heard before; an argument from reason, that “whore” according to Martin Luther who should be trusted with nothing (even though, oddly, it is the only thing Sola Scriptura protestants depend on). The point being that before St. Paul wrote their favorite passage in Second Timothy, he had already demonstrated convincingly that Scripture alone was incapable of resolving a conflict. If you recall in chapter 15 of the Book of Acts, there was a conflict about the necessity of circumcision. Some, relying on the scriptures, claimed it was necessary for gentile converts to be circumcised and obey the Mosaic law. Paul and Barnabas had disputed this. How did they resolve it? They went to Jerusalem, where what happened? Was the issue resolved by turning to Holy Scripture? No, it was resolved by authority of the Holy Spirit speaking through the Church. “And when there had been much disputing, Peter, rising up, said to them: Men, brethren, you know that in former days God made choice among us, that by my mouth the Gentiles should hear the word of the gospel and believe. And God, who knoweth the hearts, gave testimony, giving unto them the Holy Ghost, as well as to us: And put no difference between us and them, purifying their hearts by faith. Now therefore, why tempt you God to put a yoke upon the necks of the disciples which neither our fathers nor we have been able to bear? But by the grace of the Lord Jesus Christ, we believe to be saved, in like manner as they also. And all the multitude held their peace” (Acts 15:7ff).

The protestant argument falls apart, not just because it is contradicted directly by scripture, but also because St. Paul has demonstrated that it is insufficient alone to be used in the context of resolving doctrinal disputes.