With how much Credence fawns over "Mr. Graves," Grindelwald thought that it would be simple to seduce him. However, when he goes to touch Credence for the first time, he's surprised to see Credence is scared. After a bit of prodding, Grindelwald finds out that Credence isn't a virgin because he was raped before he met him. Grindelwald decides to take things slow to show Credence that sex doesn't need to be painful. And to prove that he'd never rape Credence, he goes and hunts down the person who raped Credence and kills him in as painful and drawn-out a way as possible. It's definitely because this person ruined Grindelwald's plans, not because of any actual affection he might feel for Credence (in other words, it's totally because he cares about Credence, even if it's just in a possessive way).