I'd recommend listing your deceased father-in-law first, since this is a joint return and he was listed first in previous joint returns. This may require printing and filing the return by mail, but assures some continuity insofar as the IRS' records of his meeting his tax filing requirements.
In the IRS instructions for Form 1040:
"If you filed a joint return for 2019 and you're filing a joint return for 2020 with the same spouse, be sure to enter your names and SSNs in the same order as on your 2019 return."
Deceased Persons – Filing the Final Return(s) of a Deceased Person
Listing your mother-in-law first is probably just fine, but she may still encounter issues with the PIN requirement and e-filing. Changing the established name order isn't the end of the world, but it could result in processing delays for your taxes.
