I believe that Margaret DID know of the need for a Starborn. I don't believe that Thomas was her first attempt. It think she was just enjoying great sex.
But, it's entirely possible that she learned of the need, and maybe the process, for creating a Starborn, from Pappa Raith's library. And then she started working on a means of escape.
Further, I believe that Justin was in on the plan.
Here's a further WAG ... Margart was trying to get the Vampire courts together to take over the outer gates.
I don't think she ran off WITH Malcolm. I think she met him while on the run.
I think she was trying to create a starborn with LR. She told Eb that she was with LR to accomplish something, that they had a plan.
I think it more likely that Elaine's parents didn't know, but someone (Justin) saw the circumstances of her birth and figured it was possible. He then killed the parents and arranged to become the foster parent. IIRC he adopted Harry for pretty much the same reason.
In Blood Rights Ch 35, Eb clarifies a few of these details:
I don't know why, but for some reason she turned away from her previous associates, including Justin DuMorne. After that, no where was safe for her. She ran, from her former allies and from the wardens for perhaps two years... She met your father. A man, a mortal without powers, without influence, without resources, but a man with a good soul like few I have ever seen. I believe she fell in love with him.
Combined with what Eb tells about the dinner with Margaret, Lord Raith, Ariana and himself in the last chapter of Changes, we can infer a few facts:
- The attempt to conceive a starborn was a deliberate plan involving, at a minimum Lord Raith and Ariana. Justin was also a likely co-conspirator.
- She met Malcolm after leaving Lord Raith, not before. Which isn't to say she didn't deliberately seek out a man with a "good soul."
In DuMorne, Raith, and Ariana of RCV, we have three known Outsider associates. Whether the starborn plan originated from one of them or from Margaret, it seems likely that learning of their Outsider associations / plans for her potential child were what drove her away. Leaving Thomas behind means she didn't leave simply out of mother's love / "You won't harm my baby," so it's more likely she left with the deliberate purpose in mind to subvert their pro-Outsider agenda. It is possible / reasonable to think she thought out someone like Malcolm for just that end. Or maybe the father didn't factor in, hard to say. The conversation with Malcolm in Dead Beat suggests he's at least in on the plan post-mortum, but there's no evidence either way if he had knowledge of it before his death.
The assumption that this triumvirate had something to do with Malcolm's death is reasonable. What I am curious about is if Elaine was known to the rest of the group, or only Justin. And if she was similarly cultivated, or just come upon by Justin?