The thing is, no-one knows that Ralph killed Pie-o-my. Its one of those things that was left open to interpretation on the viewers part.
I'd imagine Tony was under the impression that Ralphie killed the horse for a number of reasons; Ralphie hasn't exactly been the most controlled person in the family (Killing Tracy, turning down a drink with the boss, taking his time with the Jackie jr situation, disobeying Tony's orders to not draw attention to the garbage buisness...), he did just break the news to ralphie about him seeing Valentina and staright after that well-timed news....Raplhie fobbed off responsibility of Pie-O-My on Tony.
Don't forget, Tony never liked Ralphie. I think Tony took Ralph as the obvious scapegoat, and given Raplh's history......Tony acted on impulse (which Dr.Mefli wouldn't be too happy about )!!