Separation of Church and State was there to protect religious freedom from the state, since only the State can make laws, have an army, and control the laws and jails. A Church can organize citizens, make arguments, and appeal to emotions, but that is not the same level of power as having tanks, aircraft carriers, swat teams, prosecutors and judges. I don't understand the position of the left, since they think the 100 pound weakling is a threat to the 200 pound football player.
The Roman Catholic Church; Holy Roman wEmpire, before the 1400's, had an army and could leverage countries. But those days were long gone by the time of Jefferson, three hundred year later. By his time, States were using churches as a political tool; Church of England, because the power of the original Roman church was dissociating and diminishing.
The real perceived problem for the left, is their own moral corruption. A moral POV, from a church with too much clout, would have an adverse impact on their schemes and political orientation. This is why the Democrats, under then Senator Johnson, made a law that said a church could not maintain its tax free status and also be political. The Democrats found it easier to lie and cheat without a trusted referee. It had nothing to do with the church building an army or wanting nuclear weapons so they could take over the reigns of power. It was about moral truth not mixing well with political schemes and scams.
President Trump removed that law that prohibited religions from the political process. One can see some of the impact, already. The swamp is now under moral judgement, which appears to have the most impact on the Democrats. This judgement is starting with sexual misconduct, and will spread from there to other forms of lawlessness and corruption. That was always the real fear of the left. Over the past several decades, they needed a scam that made religion appear to have the army and not just a truthful voice.