This is pure speculation, but I believe he meant she would protect everyone as they were going to enter the final battle with Naraku. In the Japanese version, he actually says that "I wanted to protect her forever," not the other way around, so this is something that only appears in the English dub. However it could also refer back to Inuyasha and Kagome. Kikyo has known for a while now that Kagome also holds a special place in Inuyasha's heart and she also knows that with her death, Inuyasha and Kagome can now be together without anyone holding Inuyasha back. I think that's what she wanted: for Inuyasha to be happy even after her death. And she was finally at peace with dying, not only because Inuyasha came for her, but because she knew she would be happier in her next life.