I think Tony resents Baccala's happiness and apparent stability as a family man. His real family, not his mob family. Bobby seems to have more morals than any of Tony's other associates. He loves his kids. He cried like a baby when he lost his wife. And he took care of Junior like he was caring for his own father, he even bought him stool softener.

Tony seems to resent other people being happy, especially within his own circle of friends and family. I think he's enjoying holding this kid's murder over Bobby's head. As if to say "Hey Bobby, look, you're no better than me."

Then again, Tony's motives are Melfi's job, not mine.