The Harley Quinn series is a comedic take on Batman's greatest enemies. While the show maintains the personality traits that make the characters so iconic, they're satirized to the point that they are seen as anything but evil. A great example of this is Scarecrow, who shows a much softer side to his character, but in Season 1, Episode 13, "The Final Joke," his nicer side leads to an untimely and unjust fate.
During the episode, the Joker manages to capture Batman and take over Gotham City for his birthday. However, he still feels unfulfilled as a person and wonders what's next now that he has gotten everything he ever wanted. As he stews in his negative thoughts, the Scarecrow comes in to provide some optimism to the dour scene.
He tries to remind Joker that he's accomplished so much in his life, and there's still more that he can achieve. Instead, the Joker thinks about Harley Quinn and how much debauchery they committed after a night of crime. To try and help lift his friend's spirits, the Scarecrow does the unthinkable and unmasks Batman.
Almost immediately, the Joker gets even madder as he and Batman's relationship was based on the mutual chase between each other. Unmasking the Dark Knight was never anything that he wanted, and by learning his identity, the one thing the Joker had going for him was ruined. So rather than scold Scarecrow, the Joker sprays him with acid from his flower, melting his friend's face and killing him.
While the act is fitting for someone like Joker, Scarecrow didn't deserve such a cruel demise. He only ever wanted to make the Joker happy and was even apologetic after unmasking Batman. However, because Joker is incapable of love, he cannot appeal to any humanity within him. Sadly, Scarecrow only served as an example of how not to treat Joker or risk facing a similar fate.
Harley Quinn could be considered a disarming look at Batman's enemies. As a result, the moments that make them seem as evil as they truly are can be surprising. For Joker, many of the things he does are inherently funny through the lens of the show, so to see him kill another villain so cruelly makes him only look more evil. Scarecrow was a good supervillain "friend" to Joker, and his well-intentioned, whimsical choices were often made with the best intentions. As a result, his death serves to make audiences dislike the Joker more and evoke pity for a character that didn't deserve the death he got.