I would say the grand majority, yes. I would not deny that there may be a few out there who just didn't understand what they were doing, but those are far and few between. In my experience in talking with church leadership, they full-well know what they're doing, and/or they simply do not care because they get to rake in the cash, and I also agree that most of them are not Christians.
The bottom line is that there is no foundation of repentance (i.e. grief and godly sorrow of wrongdoing) in their hearts, and because there is no repentance, there is no salvation because God resists the proud of heart; He only gives his grace to those who have been humbled to repentance and have a contrite spirit (i.e. a spirit that has been broken-hearted in grief over their sin).
The LORD is nigh unto them that are of a broken heart; and saveth such as be of a contrite spirit.
-Psalm 34:18
But he giveth more grace. Wherefore he saith, God resisteth the proud, but giveth grace unto the humble.
-James 4:6
What many are doing is claiming with their mouths that they follow the Lord Jesus Christ, but in their hearts, they are far from him:
This people draweth nigh unto me with their mouth, and honoureth me with their lips; but their heart is far from me.
-Mat 15:8
Jesus told us that, on the Day of Judgment, there would be many who would call him "Lord," meaning that they claim to be His disciples, but Jesus said He would tell them the truth, that He never knew them, and that is because they never came to the grief and sorrow of repentance:
Not every one that saith unto me, Lord, Lord, shall enter into the kingdom of heaven; but he that doeth the will of my Father which is in heaven. Many will say to me in that day, Lord, Lord, have we not prophesied in thy name? and in thy name have cast out devils? and in thy name done many wonderful works? And then will I profess unto them, I never knew you: depart from me, ye that work iniquity.
-Mat 7:21-23
Notice that He said MANY, not few. He also said that few would find the way to eternal life, but MANY shall go the way of destruction:
Enter ye in at the strait gate: for wide is the gate, and broad is the way, that leadeth to destruction, and many there be which go in thereat: Because strait is the gate, and narrow is the way, which leadeth unto life, and few there be that find it.
-Mat 7:13-14
Thus, to understand 501c3 is to understand it is only a symptom of the underlying cause. The underlying cause is greed, extortion, excess, and a general sense of wicked men who are hirelings that make merchandise of the people:
But he that is an hireling, and not the shepherd, whose own the sheep are not, seeth the wolf coming, and leaveth the sheep, and fleeth: and the wolf catcheth them, and scattereth the sheep.
-John 10:12
And through covetousness shall they with feigned words make merchandise of you: whose judgment now of a long time lingereth not, and their damnation slumbereth not.
-2Pe 2:3
And so, as you have rightly pointed out, the church leadership was leavened LONG before they signed a 501c3 contract, and so I hope you now understand that, if you want to be sanctified by Christ, you should look to join up with an unleavened church, and I will warn you, that journey can be much more difficult.
