Question: Why did Sideshow Bob frame Krusty?
Question: Why does Sideshow Bob not want to pursue Lisa since, if it hadn't been for her pointing out to Bart all the major flaws in the CCTV footage that would show that it couldn't have been Krusty (in Krusty Gets Busted), he wouldn't have been found out by Bart and Lisa? He knows Lisa is smarter than Bart, so surely he would have realised that Lisa was the brains behind the detective work that got him caught.
Question: How come Sideshow Bob only wants to kill Bart? In "Krusty Gets Busted", Bart and Lisa together investigated the crime and concluded that Krusty was framed. So Sideshow Bob should be going after Lisa too.
Answer: Essentially Bart was the main figure behind Sideshow Bob being arrested and convicated. While Lisa helped Bart gather some of the clues, it only lead them to the theory that someone else was behind the robbery. It wasn't until Bart noticed the size of Bob's feet compared to Krusty's feet that he discovered it was Bob who framed Krusty.
Chosen answer: He wanted Krusty out of the way so he could host a show where he isn't the constant fool.
Captain Defenestrator