In "University", when Tony hits Ralphie behind the Bing!, it's not because he's killed Tracee but because he casually shrugs it off as just another by-product of This Thing Of Ours: "It's my fault she's a klutz?" In "Whoever Did This", the moment at which Tony hits Ralphie is after the latter questions Tony's emotional investment in an animal, referring to the fact he eats "beef and sausage by the fucking car load".
Both times, Tony lashes out in response to being faced with his own moral contradictions and having them exposed. That the first of these scenes happens in front of others and that the second scene is private shows that it's not about 'saving face' for Tony, it's something much more simple and childlike. When forced to face his own emotional immaturity, he turns to violence. We see him do it time and time again with Melfi whenever she approaches anything resembling 'progress' in Tony's therapy.
Ralphie is a hoodlum in extremis; worse than merely a loose cannon, he's rational with it. He's very clever, and it's a great, intelligent performance by Joe Pantoliano.
Tony is a highly dysfunctional, self-destructive character; he kills Christopher too without much calculation. In the Season 6B episode "Remember When", he also tries to force Paulie into admitting to something he already knows but doesn't care about (the Ginny Sack joke), so that he can justify killing Paulie for becoming too porous under pressure - an increasing worry with the FBI chasing would-be informants - but when Tony sees the scenario through and has to finally deal with his own irrationality, he settles for a babyish compromise: he violently throws a bottle at Paulie for him to catch - you can liken that sort of reaction to when he punches the wall in "Whitecaps" when Carmela tells him of her fantasising over Furio.
I don't think Ralphie was 'living on borrowed time' anymore than anybody else living on Tony's periphery, and I don't think the reason for this 'borrowed time' is anything to do with Tony's moral logic. The ambiguity as to who Tony is referring to when choking Ralphie to death and saying, "She was a beautiful little creature, what did she ever do to you? You fucking killed her," is telling: Tracee or Pie-O-My? Does it even matter when the reasoning is so irrational anyway?
