I’m going to play a bit of Devil’s Advocacy here regarding people Tony has killed or had killed:
Pussy - Pussy was actively engaged in an activity that would, if brought to its logical conclusion, lead to Tony being arrested and put in prison. He was actively working against Tony and the Family. He was a traitor, plain and simple. Regardless of whether it was objectively right for Tony to kill Pussy, it’s definitely something that people can understand and feel sympathetic towards. Your best friend betrays you and takes actions that will likely destroy your life. That’s bad.
Tony B - His crimes were essentially the same as Pussy’s. He knowingly and willingly took actions that he knew his cousin and Boss would not approve of. If it became known that he had performed those actions, his cousin and Boss would likely be enveloped in a shitstorm. He did it anyway. (I think Pussy’s transgression was worse, since he betrayed not just people but the very ideals that their society was based upon.) Moreover, as Stratocaster points out, Tony S. killed Tony B. so Phil wouldn’t get to torture him. That’s definitely a noble motive.
Ralphie - Ralphie was a great character, but I don’t think very many viewers sympathized with him in the slightest. Recall how he treated his stripper friend. The other mobsters didn’t even like him much. Even among scum, he stands out as scummy. So when Tony attacked Ralphie for destroying Tony’s horsie, the audience was definitely rooting for Tony to win. While killing someone because they hurt an innocent animal may well be taking things too far, it’s a hugely more sympathetic than beating and killing a stripper after emotionally abusing her. (And violating the codes of the social circle you run with while doing it!)
Jackie Jr. - This is harder to defend than the others. The audience will instinctively sympathize with being angry at betrayal or the murder of a pet. They will also understand that someone who kills a member of your group will need to be punished. But the killing isn’t planned (things just got out of hand), and the killer is a youngster, and he was doing something very similar to what Tony had done many years before. Moreover, his death would cause significant emotional pain for Meadow. Still, I think Tony gets an instinctive partial pass on this because he didn’t pull the trigger himself. Indeed, when he told Ralphie to get rid of Jackie Jr., he said it by not saying it. And Ralphie doesn’t even do the killing, it was Vito. So Tony is at least a couple of steps removed from the killing.
Also, I think most viewers simply didn’t sympathize with Jackie Jr. the way they do with Vito. Jackie Jr. grew up as the son of an important member of the mafia (for a while the acting boss of a family). He’s a bit of a prick, and thinks he’s tougher than he is. He’s similar to the “spoiled rich kid” archetype. Vito, on the other hand, has lived a lie for years. A single wrong move and his life as he knows it is over, one way or another. He has to have a wife and a girlfriend to keep suspicion away. He comes across as the “rough on the outside, but gentle on the inside” type, which instinctively gets sympathy.
I agree that in the overall scheme of things these are all bad people. They’re mobsters. They kill. They maim. They steal. Etc. But most of Tony’s killings thus far are easily understood and sympathized with, even if they’re not forgiven. If Tony kills Vito we may understand, but it will be difficult for us to sympathize.