On the one hand she does not want the Jedi to be killed until she does at the end
As I understand it, Kreia didn't want the Jedi Masters dead; she wanted them proven wrong. That's why she's pissed if you kill the Jedi yourself - she wants to change them, not get rid of them. Killing your enemies, in her mind, is a hollow victory unless there's absolutely no alternative. Kreia alludes to this on Nar Shaddaa, where she teaches the player to feel the mass of life on the planet. She says that the greatest victories are not even manipulations, but rather, as she puts it, "awakening others to the truth of what you believe."
That's what Kreia wanted to do. She wanted to convince the Jedi that they were wrong, and for her, that was much better than simply killing them. Kreia only kills them on Dantooine (if light-sided) because they were attempting to cut the Exile from the Force. Defending her son from the bullies, as Scorchy put in in his analysis.