Fair enough, but if it's that much of a disaster it might as well keep going. More likely they would actually just count the electors as "Democrat and Republican" instead of by person and go from there, but if they didn't happen there's no way they'd respect the electors.
I'm thinking you dont understand the process here?
State governments certify lists of electors before the election. When people vote for the candidates they are actually voting for the list of electors in their state. So if I vote for Donald Trump in Maryland, I am actually voting for the list of electors who have signed a pledge to cast their votes for Donald Trump. Generally speaking state law says that the state is required to certify the electors chosen by the vote. Changing state law after the election would result in one hell of a lawsuit and probably result in a lot of impeachments.
So if Hillary Clinton and Tim Kaine are in the same plane and it crashes on November 7th, the democrats would just scramble to pick a new candidate in a hurry. Then Obama would go on the TV and tell people "Everyone, cast your votes for Hillary Clinton and when you do it will be a vote for Biden/Warren/O'Malley and a vote to stop Donald Trump." And because it would be the news story of the century, everyone would pay attention and every news anchor in the country would explain constantly that a vote for Clinton/Kaine is actually a vote for whoever.
Then the vote would happen (and probably favor the democrats) and after the election all the Clinton electors would have plenty of time to talk things over and make sure they all agree. Then they cast their votes in January for whoever they pick. You might have a bunch of lawsuits at this point in the process between November 8th and January in which case all sorts of constitutional law comes into play but I'm thinking it's unlikely the courts change the result.
At no point in the process does congress enter into it.