I don't think any churches should receive tax money, as your post notes they did in the early 1800s. The fact that Massachusetts churches might have argued to stay on the public dole doesn't make it right or indicate that Jefferson supported that specific action.
Jefferson's Unitarian church may have differed considerably from the Massachusetts Unitarian churches. The three Unitarian churches I've been to in different parts of the country were quite different.
One need only read about the European wars of religion that preceeded the development of our Constitution to see the dangers of state sponsorship of religion. If you didn't belong to the state church, in some places you were in danger of being burned at the stake or prohibited from holding services or having your churches destroyed. Toleration of other religious beliefs or nonbelief was slow in coming and is still hard for some to accept.
The Unitarian church of today has little to do with the Unitarian church of Jefferson's time. If you read Channings sermons, Adams writings, the Jefferson Bible, the works of Priestly,Theophilus Lindsey and other antitrinitarians you will see they were all on the same page. No Buddhists, no wiccans, no atheists wandering the aisles of the Unitarian churches back then. They all considered themselves Christians (many other Christians did not however).
The intent of Jefferson and others was to encourage religion, not limit it. The only restriction was that there would be no Federal church. All the founders agreed that a religious moral citizenry was essential if a democratically elected constitutional republic were to survive. The first amendment was an antitrust act of sorts, the purpose of which was to allow all religions to flourish and be vigorously debated in the public arena.
An analogous system was devised for the states. Federal power would be limited, experiments in democracy would take place in all the states and the best system would be, naturally, copied by others.
Btw... the lyrics of the Battle Hymn of the Republic were written by a Unitarian. I doubt a UU of today would pen the words the radical Unitarian feminist Julia Ward Howe did in 1861:
In the beauty of the lilies Christ was born across the sea,
With a glory in His bosom that transfigures you and me:
As He died to make men holy, let us die to make men free,
While God is marching on.
How can you say that? I simply don't get it. If they wanted separation of church and state, the founders would have put it in the constitution. They didn't. The concept was not written into constitutional law until 1947.
While you, like all of us, have opinion on what should be, to claim there is a constitutional basis for your opinion is simply not the case. You can't take one phrase out of a letter Jefferson wrote and claim it has legal validity. It doesn't. Do you think the letter Jefferson wrote expressing the desire that all Americans become Unitarians has any legal standing? That the government should try to fulfill his wishes and promote Unitarianism? Of course not.