Yes Jefferson had it right. But what he failed to do, was realize that cults, do not seek truth or compromise, and error remains eternal.
The witnesses are an lesser example of this. Truth left to itself can find it's way, but in the witnesses, the governing body owns it, and it's not up for debate. This board, has been free in seeking that truth.
His comments however, preceded the Barbarry wars of 1801 to 1805, when Muslim pirates were boarding his ships and demanding they pay tribute.
Jefferson obtained a copy of the Koran and studied it to try and reach a negotiation and avoid more bloodshed. Here, he discovered that compromise was impossible, just as we see today, in all the Jihadist wars. This lesson has largely been forgotten.
The principles of freedom were derived from the Judeo-Christian ethics and today we see Keith Ellison swearing on the very koran that Jefferson studied!
In France the witnesses are recognized by the government as a cult. I think that his idea of religious freedom should not extend to cults, and should have been revised after the Barbarry wars.