Right before that, he states, "Difference of opinion is advantageous in religion. The several sects perform the office of a Censor morum over each other. Is uniformity attainable?"
The implication is made more clear when read in context. He is understood to be talking about one denomination or faith or religion or sect (or whatever you care to call it) taking control of all religion. He saw the benefit of a "marketplace of ideas' even in the religious realm - a democracy within religion if you will.
Personally, I could care less if you blast religion or Christianity. Truth is, Jefferson was not a Christian by the standards of our day or really even by the standards of his day.
He certainly did, he also said, "In every country and in every age, the priest has been hostile to liberty. He is always in alliance with the despot, abetting his abuses in return for protection to his own."
Actually to be honest I don't see how your context changes the message in any way at all? Yes he was saying that diversity of religious beliefs is better than attempting to make one single religious belief supreme over all. But it still in no way changes the statement he is making in the sentence quoted above.
Certainly Jefferson had this thing about fanatical, intolerant and superstitious manifestations of Christianity, and he had a horror of Calvinism which I can identify with- the grotesque idea of predestination. His going through the New Testament revealing all the miraculous claims was also a bold thing to do at the time. Great chap, Jefferson, one of the men I admire the most.