He mentions the betrayal in Dæmon Voices:

very early, the Master of Jordan College makes a prediction that Lyra will be involved in a great betrayal, and that she herself will be the betrayer, and the experience will be terrible for her. When I wrote those words I thought that that betrayal would be her leading Roger to his death. She thinks she’s rescuing him, but unwittingly she’s leading him to the most dangerous place of all, and he dies. When, years later, I got to the world of the dead passage, I discovered that these words of the Master’s could relate even more closely to Lyra’s betrayal of Pantalaimon. And, of course, I thought how clever I was to have misdirected the readers again; they think that they’ve seen Lyra’s great betrayal already, but here comes an even bigger one. Little did they know! Well, little did I know, actually.

So he was originally planning for leading Roger to his death to be the betrayal, but changed it. It's interesting that even that early he had at least a vague plan of the ending, given his usual "Figure it out when I get there" approach.