Assuming the scandal with Clinton was bad enough that she ended up with only a few % of the P.V., this is what the map would likely look like. Turns into 2020 with GA+FL switched. At the same time, why wouldn't most Clinton supporters endorse Stein in this scenario?
First of all, with OP saying "something happened" to both Clinton and Kaine, I figure it would be more like they were both assassinated towards the very end of the campaign, with no time to replace them on the ticket. Not a scandal.
In that case I think there would be mass sympathy towards the Democrats and mass outrage towards Trump, especially if one of his "Second Amendment people" was the perpetrator. I think rather than endorsing Johnson or Stein, people would still be encouraged to vote for the Clinton ticket which I think would win in a landslide, with the Democratic electors instructed on who to replace them with after the fact. Biden is actually a strong possibility to become president.
Also I for one would have rather voted Johnson than Stein in any case.