Oh, you might be correct. I just looked up the timeline. I always thought that she met Malcolm after her escape. Now it makes sense: she needed to escape and leave Thomas, because she was pregnant with a non vampire child in a vampire household.
That's the one thing Eb does tell Harry about Margaret in Blood Rites, that
after she met and fell in love with Malcolm,she found the strength to leave Lord Raith.
My thoughts on Harry being planned are from IIRC two comments somewhere in the books: I can't remember who said it, but it went like "what they bred you for" (was it Nicodemus or Dracul?) and "what he was meant to be" by Martha Liberty or Listens-to-Wind in Summer Knight. This implies that Harry's existence didn't seem to be random.
@Talby16: so, Thomas wasn't planned. What a relief.
Lash spells it out for Harry in White Night, his conception was no accident, a lot of factors go into it. Now not clear was this something that Margaret thought up on her own? Doubtful since everyone but Harry seem to know what Harry is and why he was conceived, so a given that a star born would be conceived. However who, or what planned this is a bit more of a mystery. If the White Council planned it, it's doubtful they would choose Margaret, an outlaw basically, to be the mother of their star born.. Martha Liberty did say to Listens to Wind that they knew what Harry was meant to be, or more accurate they suspect, or believe, dangerous and not nice, i.e. Listen and Drakul.. However Margaret seemingly on her own again, if Lash is to be believed in White Night decided to do this after she fell in love with a truly good man, Malcolm. I think the plan was always out there, i.e. the year was right, we know now star born happen every so many years, in her usual rebellious way, Margaret chose to throw a monkey wrench into everyone's plans by conceiving a star born with a truly good man. This is what sets Harry apart from the rest of the star born, it is significant and no accident that it is repeated constantly though out the series that Harry inherited his father's good heart among other things. So there most likely was a plan out there for the conception of a star born, but when Margaret conceived Harry with Malcolm, it backfired. However I think a huge clue as to why ultimately the White Council elected to throw Harry out, is they know what Harry was meant to be, as Martha Liberty said, but they, with the exception of Eb never knew Malcolm, so they have no clue who Harry really is.
As to whether or not Thomas was planned, if we go by the information in Peace Talks he was born in the wrong year to be a star born unless there is a lot of wiggle room say plus or minus a decade. I still think Margaret knew that having sex with Lord Raith, most likely unprotected sex meant she could or would become pregnant by him, which happened. However I still think she found a way for her talent not to be passed onto any child she conceived with Lord Raith. And yes, Thomas could still have some talent, I seem to remember either Harry saying it or it could be a WOJ that everyone, even vanilla humans are born with some magical talent..