I agree that the leader having the malevolent trait is a bug. I don't think you've proven that the leader having the malevolent trait is the cause of your high crime rate. Like I said, my leader also has malevolent, but I'm seeing only a normal number of criminals, and normal methods are dealing with them.
I am currently playing as the Altarian Republic (Civ home planet Gov has ideology Benevolence) and I've seen 5 criminal citizens by turn 268 on my 3 core worlds. That I can live with and as a game mechanic keeps me on my toes. But that is not what I'm seeing in my custom civ games.
I've got five different Custom games starts that all went the same way & the only thing I can see is the Malevolent ideology. I agree you can stop it if you know what you're looking for from the start. However if you don't know it's coming & send the criminal population out to your colonies your goose is cooked. New players won't know how to deal with this.
Can you play the game save I attached in Reply #4? Please try & tell me what you think.