Everybody assumes she met Malcolm after the meeting, when the safer assumption might be to assume she met him as a result of the meeting. Holding open the possibility that meeting him was what broke her free of Raith. I've always thought the possibility that she was pregnant when she ran was high. By the time she became pregnant she had fallen in love with Malcolm. Since she knew when the baby had to be born to become a Starborn she entered Faerie and manipulated her time there to make sure the pregnancy ended at the right moment.
I have to go back and read the passage, but what I remember is Eb had dinner with Raith and Margaret from time to time.. Something a bit more casual than business, observing how Eb and Margaret interacted tipped Arianna off that they were father and daughter. Why would Margaret have met Malcolm as a result of having dinner with her father, Lord Raith, and Arianna?
Lash in White Night tells Harry that his mother found the strength to leave Lord Raith for a reason.
That reason was Malcolm, she had fallen in love with him and because of his goodness decided to conceive a star child with him. In the soul gaze with Thomas when he talks Margaret, she says she is sorry for the burden she and Malcolm placed on him. In his dream conversation with Malcolm I believe it was in Dead Beat, Malcolm says pretty much the same thing, but wouldn't elaborate on what he meant. No, it was a pre-planned pregnancy and Malcolm was very much in on the pre-planning.