The most likely replacements would be the other senior officers - the Commanders in Chief of the Atlantic and Pacific Fleets, namely Royal Ingersoll and Chester Nimitz. Both, however, were appointed only days or weeks before.
Of the two, I'd assme Ingersoll would be appointed instead because he was based in Washington, and FDR wouldn't want to appoint yet another new admiral for the Pacific Fleet (in one month there would have already been three - Kimmel, Pye as interim commander, and Nimitz) when it was vital for leadership there to be steady.
There are other candidates, but I don't know of any who would be stronger. I don't think FDR would want to reappoint Stark, Leahy was effectively Chairman of the JCS, and FDR was already angry at Pye. Who else could it be - Ghormley? Halsey is probably needed in the Pacific, and unlikely to be promoted ahead of Nimitz.