They're not being forced to do anything. If they don't want to pay taxes, like any other organization, then they have to meet the requirements for
tax exemption.

I am not the only IRS employee who’s wondered why churches go to the government and seek permission to be exempted from a tax they didn’t owe
to begin with, and to seek a tax deductible status that they’ve always had anyway
Well christ, no surprise here, government employees are complete morons. Of course a church has to apply for tax exempt status, at a minimum it has to
be demonstrated that its actually a church.

but they don’t seem to know or appreciate the implications of what it would mean to be free of government control."
What churches have been 'silenced' by this?

Jesus did indeed say, “Render to Caesar the things that are Caesar’s;” but that’s only half the verse! Jesus went on to say, “and to God
the things that are God’s.” The obvious question to be asked is at what time did Jesus place His church under the authority and jurisdiction of
Caesar (the State)?
This is poor reasoning. Jesus said that people should pay their taxes, period. The Founders of the US decided that Churches should be seperated from
the state, and not have to pay taxes. Its because of the Founders, and NOT JESUS that churches don't have to pay taxes. If that 'crazy' Jesus had
had his way, the churches would be paying taxes.