I believe any time a Government taxes any organization it's a form of Government control, I believe when you require a religion to be taxed then you are requiring the organization to show the Government how much money it is taking in and then paying a portion of that money to the Government which in my view is a form of control.
Taxes on religious institutions represent a form of government control. While the collection of taxes does not exert an overt control over these groups, it is control nonetheless. The government has authority to audit and discipline any group with pays taxes. The government can then legislate or create law to modify the rules with which it oversees these groups.
Taxes on religious institutions, if they are not framed as 'we will tax the religious institutions this way to effect the way they practice, and impose more if they don't practice right' are not government control.
The logical corollary to this is that churches that violate civil laws should not be subject to persecution on these grounds. I think we can all agree that that would make little sense.
If they are classed as charities, they need to be subject to the same constraints as other charities. They should be treated no different, as that is what keeps things fair. To NOT tax them, technically, is showing favouritism over non-religious institutions. THAT would be having laws respecting institutions of religion, favouring them over secular organizations.
Obviously, almost everything in our society gets taxed in order to provide needed government services, so religion is not being controlled if it gets taxed. Exempting it is what really sets it apart and that is not a precedent that we should set as a culture, so taxation is fine.
Taxes on religious institutions are not a form of government control. The reason I believe they are not a form of government control is because they offer degrees that many other regular universities also offer. On top of that, it would not be fair to other institutions who are already paying tax dollars.