I had this exact same issue. I had to swap the names and place the deceased as the secondary taxpayer in order for the e-file to be accepted.
There is a catch though, that I don't think I have seen other people mention. You know all those questions where TurboTax asks you "Is this (1099, etc) for (Name #1), (Name #2), or (Both)?"? Apparently what you are really answering, and what TurboTax is storing under the hood, is the answer to the question "Is this (1099, etc) for (The Primary Tax Payer), (The Secondary Tax Payer), or (Both)?". So, when you switch the names, the answers to these questions are now all wrong, and need to be swapped, as well.
