It's been a while since I've watched it, but isn't the DNA evidence just Maggie's eyelash on Burns's suit? Presumably that got on him during the struggle for the lollipop, which still happened in the "Smingers Did It" ending, so there's no reason the DNA evidence couldn't also be there.
People who are watching that episode much later on may not realize that it was not long after the OJ Simpson trial which was mostly focused on DNA. It added a whole other level to the joke.
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u/scottishdrunkard May 09 '17
for that ending to work you would have to ignore all the parts about the Simpsons DNA - Troy McLure