The Sundial Clue Further Implicates Maggie
There's one final clue that The Simpsons drops before the end of the first "Who Shot Mr. Burns" episode: the sundial. After being shot, Burns stumbles to the town sundial (already called out by Smithers earlier in the episode) and splays out pointing to south and west. While it's not resolute, the implication is that these are a nod to the gunman's identity, meaning someone with "S.W. or "W.S" initials, most prominently the (already discounted) Waylon Smithers.
However, there's an added wrinkle to this. Throughout "Who Shot Mr. Burns - Part 1", the time "3 pm" comes up: it's when Pardon My Zinger airs, when Mr. Burns enacts his plan, and multiple clocks in the background read 3 pm. This is repeated to the point it clearly conveys some importance, likely that Burns' arms on the sundial should not be viewed as a compass but as a clock from his point-of-view. That flips the initials, making them "M.S." or "S.M." The most prominent characters with these initials include Moe, Marge and Maggie (there's also Mona Simpson, Homer's mother, but her first name hadn't been confirmed at this point). We know it can't be Marge from the shooting and Moe has a shotgun so would be unlikely to take the pistol. That leaves only Maggie.
Of course, in the end, Burns dismisses the sundial and implies that's a total coincidence, but from the perspective of the show's writers it's clearly intended as a deciding clue.
The Candy From A Baby Clue
What's clear from all the clues discussed so far is that the script for "Who Shot Mr. Burns - Part 1" is a lot more loaded than it appears on first viewing. There's a lot of coded background clues - 3 pm and Pardon My Zinger - and repeated drawing attention to elements that will be important ahead of time. This becomes even more the case in "Part 2" when there's repeated highlighting of original scenes in a bid to allow audiences who've not given the mystery much thought over the Summer since The Simpsons season 6 finale a way to catch up.
This means contextual clues should be given weight, and few are bigger than Mr. Burns wanting to steal candy from a baby. Earlier in the episode, he describes stealing oil from the school as like "taking candy from a baby" and, coincidentally seeing a baby with a candy cane, decides to go grab it. This is something that's ostensibly there to chart Smithers' downfall, but also provides the much-needed explanation for why Maggie would be in a position to shoot Mr. Burns; the episode has established he would go for a child, and when she's put in her car seat Maggie is holding a green lolly (which she doesn't have after the shooting).
"Who Shot Mr. Burns" may be something of a gimmick, but fitting of it being slap-bang in the middle of The Simpsons' Golden Age, it undeniably works. The mystery is solvable and, while even the show has mocked the slight contrivance of the solution multiple times since, the whole mystery remains captivating almost 25 years later.