Wouldn't surprise me if the show was filmed on Super35, and was designed to be framed either way. JMS has certainly done this in the past with Babylon 5. Which is considered more correct it's hard to say, barring a comment from JMS, and I don't know that I've seen one on the issue about Jeremiah.
For the record, on the non high def channel of showtime, the show indeed was broadcast 4:3. (And the second season appears to be that way too). Don't know what the more intended ratio is supposed to be though. For that matter, I don't think the first season was even shot HD, but was merely...