There is no “scriptural justification for withholding fellowship” merely because brethren use cups, classes, and instrumental music. To do so on this basis is anti-scriptural, unscriptural, and unreasonable. It indicates a lack of knowledge or understanding of fellowship and is usually justified by a misuse or twisting of the scriptures motivated by the party spirit.
Those who withhold fellowship on this basis fail to understand that fellowship is not a matter of approval or endorsement, a matter of agreement on doctrine or interpretations or opinions, a matter of being right or wrong doctrinally, or a matter of knowledge. It is a state of being in Christ to which we are called by the gospel and wherein we are to be forbearing in love with one another. To withhold fellowship, so to speak, is only to be done in the most extreme cases and disagreement about items such as the three mentioned in this question do not fit into that category.
These issues change with the party. About four decades ago a brother in Colorado wrote an article declaring “justifying” withholding fellowship from those who use instrumental music. I wrote him a letter asking him several questions pointing out that the same arguments and scriptures he used to oppose instrumental music could be used to oppose cups and classes which were used by his congregation. He sent me a terse reply, to say the least, saying in toto saying that my questions were an insult to his intelligence.
I have beliefs about the items mentioned in this question but I have learned over the years that it is possible to share life in Christ in a peaceful and productive way in a congregation of saints with brethren who differ with me on these issues. For example, a few years back a brother came to me and said that he thought it was scriptural to use cups and classes, but would like to assemble on a regular basis with the saints in Armona. He said that he would not be contentious or cause trouble over the issues. He didn’t. In fact he was a blessing to the congregation. He was a good song leader, a dynamic speaker, and participated in other activities of our assembling as well as helping in personal work.
In addition to what I said earlier about our erroneous and sinful practices relative to fellowship, we further compound the wrong by making sweeping classifications. Masses of people and whole congregations are disenfranchised because they do not subscribe to our unwritten creed. There are no scriptures that endorse our making sweeping classifications relative to fellowship of believers.
We have used fellowship as a tool to try and impose by coercion and force our interpretations/opinions relative to “disputable issues” upon brethren in Christ. Obviously it hasn’t worked. They’re good enough for God to accept, but too bad for us to welcome as He did.