"Rend unto Caesar that which is Caesar's. Rend unto God that which is God's." This would be a relevant scripture. It would suggest that a Church should reject all government control of its congregation, as people are made in the image of God and go to God. It also suggests that a Church should pay any required taxes, as, taken in context, it referred to the fact that the image of Caesar was on coins (money) and that, therefore, money (taxes) should go to Caesar.
But scripture never addressed the issue of a government that created separation of Church and State and chose not to tax churches. That idea didn't happen until after the American Revolution. So, in the US, it is legal and accepted for a Church not to pay taxes or even file tax returns. The US Government believes that religious freedom extends to a church to the point where the Church has no accountability to government around how it uses its money.
So you might say that the US Government has already rendered its interpretation of scripture: It has said that money that goes to the Church belongs to God, and not to the government. Rend unto the Lord what is the Lord's. Filing for the appropriate tax exemption makes this possible.
One note: All honesty in the collection and use of charitable donations, adhering to GAAP (Generally Accepted Accounting Principles) is scriptural. It falls under keeping the commandments not to steal and not to lie.