I thought Mac Jesus what lightweight trollin at first, but after thinking about it, I do think Walt probably killed the kid. He was desperate and he knew he had to turn jessie on gus or he was dead meat. And Walt let's not forget has done some sinister shit.
Also, I always keep this in mind...originally when jessies girlfriend OD'd and Walt could have saved her but chose not to, the writers actually originally had the script that when Walt went in the room and they were passed out HE himself injected the lethal dose into her and murdered her. But the big AMC execs made them alter it a bit. That has always stuck with me after learning that, Walt has become a selfish, ruthless murderer when it comes down to it. He'll do whatever it takes and the one way he knew jessie would turn on gus was the kid. He tried talking to him over and over and jessie just wouldn't get it. Something dramatic had to happen.
There is supposed to be some crazy ending this season. Makes perfect sense.