One thing to bear in mind is that the meaning of the First Amendment was still being debated in the early years of the Republic. No-one flipped a switch and boom all traditions of state religion were extinguished. I wrote a comment on a similar subject here; for example, though some early presidents balked at invoking God in their official capacity (Jefferson), others did not.

And, laws against blasphemy, which would seemingly be inconsistent with church/state separation and with free speech, survived into the 1950s. See Joseph Burstyn, Inc. v. Wilson, 343 US 495 (1952) (blasphemy law unconstitutional on free speech grounds).

I wouldn't want to dissuade others from answering more in depth. These are just examples showing that 1789 was not a line-in-the-sand on the matter.