A true lack of freedom would be if churches were forced to be non-profits & therefore abide by these IRS regs. They are not forced. When they accept non-profit status, they accept the limitations.
The Govt has given them an out. Whether a church chooses to exercise that option is completely up to the church.
Ha! The fact that they have to choose which of the IRS classifications they want to be in shows their lack of freedom. This argument reminds me of something I ran across on DU the other day.
In my opinion, a true lack of freedom is the government requiring you to fit into one of their classifications. The "give-up-your-property" group or the "give-up-free-speech" group. In either case you lose and the government wins. That's slavery.