Think about it this way. Does God want us to do everything that He said? Of course. He repeats that dozens of times. Here are a few, just to remind you:
There isn't anything that God told us to do that He doesn't want us to do or that He will allow us not to do. So if we don't do something that God wants, what is that? It is sin. Do we have liberty to sin? Again, of course not. When we sin and will not repent, we are to be disciplined out of the church. We are to be separated from.
Exodus 15:26, "And said, If thou wilt diligently hearken to the voice of the LORD thy God, and wilt do that which is right in his sight, and wilt give ear to his commandments, and keep all his statutes, I will put none of these diseases upon thee, which I have brought upon the Egyptians: for I am the LORD that healeth thee."
Exodus 24:3, "And Moses came and told the people all the words of the LORD, and all the judgments: and all the people answered with one voice, and said, All the words which the LORD hath said will we do."
Matthew 4:4, "But he answered and said, It is written, Man shall not live by bread alone, but by every word that proceedeth out of the mouth of God.
Matthew 28:20, "Teaching them to observe all things whatsoever have commanded you: and, lo, I am with you alway, even unto the end of the world."
So, fundamentalists and evangelicals say that certain sins are not worth separating over. Based on what they say and write, we understand that we must rank the teachings to determine which ones are worth separating over. Some say that it is only the gospel. Others add other Scriptural teachings that necessitate separation---a few more than the gospel, perhaps the "fundamentals." With this being their practice, is their anger justified when they say that they really do believe that every doctrine and practice in Scripture is important? I don't think so. Until they are ready to separate over everthing that God says, they should stop showing their faux indications of anger when we say that they don't want to believe and practice all of God's Word.
The inconsistency in the belief and practice of separation and unity, due to the wrong ecclesiology, is bad enough, but what are other consequences of these contradictions?
More Rampant Sinning
"Evil communications corrupt good manners" (1 Cor. 15:33), that is, evil companions corrupt good behavior. When we do not separate over those "less important" doctrines and practices, we become the companions of the violations of those doctrines. Churches will become more sinful and more worldly when they won't separate over sin and worldliness
Corruption of the Gospel
We are saved by grace through faith in Christ alone. However, we must have the proper understanding of grace and of faith and of Christ. We know we can have a fraudulent grace, faith, and Christ. God's grace saves from sin. Faith is not merely intellectual acknowledgement of facts. Jesus is holy. All the doctrines and practices of the Bible are consistent with the gospel, so also with the right view of grace, faith, and the Lord Jesus Christ. A grace that doesn't change someone is a fraud, perhaps mere license. A faith that doesn't work is dead. The Jesus that Heads the church wants His church kept pure. The Lordship of Christ and repentance have us turn from something to follow someone. We turn to His way, which is represented by all His Words. He is Lord, which means we follow everything that He said. The gospel connects to all of this. Corruption of these also corrupts it.
Devaluation of Doctrine
Ephesians 4:5 says our unity is based on faith. When faith is not the basis of unity or for separation, then the doctrines that God told us to believe and practice are devalued. Something else will take the place of doctrine---politics, feelings, and experiences are three common new priorities.
Misrepresentation of God
God is pure. His doctrine and practice is pure. God does not deny Himself. His doctrines and practices will not deny each other. When we are not pure and our doctrines deny themselves, that reflects on God. Israel was God's glory. Churches are also His glory. When they won't align with Him, He is tainted by their belief and practice.
Elevation of Unscriptural Institutions
When we take separation and unity away from their place of Scriptural practice, the church, we elevate unscriptural institutions. They begin to wag the church. Churches have taken a back seat in deciding why and how we separate and unify. The unscriptural institutions (colleges, boards, publishers, seminaries, conferences, associations, schools) wield more influence than churches. The Head of the Church, I'm sure, is jealous. You know what happens when He's jealous.
Disobedience to the Great Commission
Matthew 28:20 tells us to teach to observe all things that Christ commanded. The new unity says "observe the important things." We can't fulfill the Great Commission with that alteration, so we don't make disciples, true ones anyway.
Loss of True Separation and Unity
True unity and separation can be had in a church if the wrong view would quit interfering. God wants that purity and that togetherness, that holiness and one accord. The contradiction results in something entirely different. I like to say that the unity looks more like what we see at most family reunions. The separation would probably look like what happens on a plate when the gravy escapes the mashed potatoes and invades the jello.
These consequences should get someone's attention. We are living, as many have noticed, in a narcissistic culture and age. Men are less interested unfortunately in obedience to Scripture as having a niche in some peer group. I'm hoping that this will help some to reconsider and others to be strengthened by God's truth.