Why wouldn't Jefferson then go on to say that there should be separation of church and state within the individual states? The two positions of championing states rights and supporting separation of church and state within those states is not mutually exclusive.
Why shouldn't states also uphold religious freedom by separating church and state? Why would you want to live in a state that imposed religious faith on its citizens? It would appear that some of our most contentious states have the strongest language regarding separation of church and state in their own constitutions!
Because it wasn't up to him. Nor was the federal Constitution, which he had nothing to do with.
Your problem is that you simply ignore history in order to cling to your leftist delusions. The Bill of Rights was not applied to the states until after the civil war. That does not change the fact that the First amendment does not reach beyond forbidding the establishment of a religion. This was the doctrine extended to the states, not the nonexistent principle of complete non-interference in anything religious, which was never the meaning of the First amendment, and so does not apply to the states either.