The general impression I get is that a particularly noxious brand of cooperation between church and state leads to the greater promotion of atheism and religious disillusionment (Europe?), religious support for autocracy (Russia), or strains of religious radicalism owing to the perception that mainstream, state-backed faith has sold out (parts of Central Asia).
As for the actual regulation of religion, I believe there are probably certain features of any social activity found to be antithetical to our attempts to create a “universal homogeneous state” that should be curtailed—this would pertain to faiths that seek to overthrow the government, subvert its authority to tax, or encourage the breaking of various laws. That said, I do believe there is a certain “right to be ‘backwards’” that should be respected, if only to blunt attempts at radical left-leaning, top-down intervention in social affairs (ie, even in an age of marriage equality, a religious group should have the right to confine its definition of marriage; the same allowance would not be made to expand it to allowing the marriage of children, though).
