Just for anyone else contemplating this: e-filing a joint return after spouse filed a separate return, even before the due date of the return, doesn't work. IRS rejects the e-file in this case with a message that spouse SSN cannot be the primary SSN on another return already filed separately.
So it looks like an amended return filed before the due date is the only way, however my experience with that is they don't really treat it as a superceding return and replace the originally filed return with it, but rather they just process it as a normal amended return which provides account adjustments to the original return (except in doing so they might bend the rules and allow things like changing irrevocably elections normally not allowed).
Next I'll have to see if e-filing an amended return to change from MFS to MFJ works or not...
