Kaine is aware at this point (according to Web of Spiderman 1) that he completely wasted his time for years persecuting Ben and protecting Peter. He probably despises Peter now just as he once despised Ben. Ben was the one who accepted Kaine, remember, but he died. The bit about Peter being a clone? Kaine knew Raptor would never accept that Ben wasn't the real mccoy, so he made a small fib. In the process, jabbing at Peter's sense of self and his bond with Ben and also his bond with Kaine. Peter prefers not to think too long on it, but if Ben IS Peter, then Kaine is ALSO Peter, and every atrocity Kaine commits is equally within Peter, and if you stretch it, Peter is at fault for those atrocities.