What concerns me most about Marle and the beginning of Chrono Trigger isn't Marle's disappearance at all, but the way in which it was prevented.
We know, based on the theories and conclusions drawn here, that when someone goes back in time, a new timeline is created instantly as soon as the time-traveler in introduced into the past. At the beginning of Trigger, we know that Crono, Marle and Lucca all go back to 600 AD, and history is changed. However, they don't all go back at the same time.
Marle is the first to go back to 600 AD. So, according to our knowledge, as soon as she arrives there, a new timeline should be created instantaneously. The old future of that timeline is discarded into the DBT, and a new future begins from that point. However, when we're playing the game, that doesn't happen (or does it?.... see below). The story of Trigger tells us that, when Marle appeared in 600 AD, they found her, mistook her for the Queen, and the search for Leene was called off. Leene supposedly dies, and thus Marle shouldn't exist in the NEW future. Without Marle existing in the NEW future, Crono doesn't meet her at the fair, Marle isn't there to travel back in time, etc. etc. My point is that the timeline should be discarded BEFORE CRONO GOES INTO THE TELEPOD TO SAVE MARLE, since Marle's travel makes a new timeline, and the same could be said about Lucca as well, since she traveled after both of them.
NOTE: I am not suggesting the Grandfather Paradox, nor an infinite loop. I am merely suggesting that only Crono and Lucca would've been prevented from going back in time, not Marle. Marle is preserved in 600 AD no matter what happens in the new future, even if she isn't born, because she caused the new timeline to be created and the old to be discarded. However, without Marle's influence in the new timeline, Crono and Lucca would not need to travel back to get her.
However, we know that this does not happen in Trigger. Crono picks up the pendant like nothing happened to the timeline, and jumps in to save Marle. Furthermore, Lucca comes back even later to save Crono and Marle. There is no indication of a new timeline being created - nothing in the present seems to change as soon as Marle travels back.
That leaves two solutions. Solution #1 would be that, what we see of Crono picking up the pendant and going after Marle is actually occuring IN THE DARKNESS BEYOND TIME. As soon as Marle get's back to 600 AD, the old future from that point on is discarded to the DBT. However, in that timeline, Crono decides to travel back to 600 AD. He leaves the DBT and ends up in 600AD to re-write history yet again. Lucca would have to do the same thing. However, that means that beings from the DBT could travel into the real world, which makes no sense because beings in the DBT don't even exist.
Solution #2, which I think is much better, is that Marle's travel back in time does not affect her existence in the future. In other words, what I said should happen above when Marle travels back happens. A new timeline is created instantly, and it is created right around Crono and Lucca in 1000 AD, but of course they don't realize it. We actually watch it happen in the game, but we don't realize it either. The reason we don't realize it is that it doesn't change anything that we can see. In the new future after Marle appears in 600 AD, Leene is still found, and she still has children, and Marle is still born in 986 AD or so, and still runs into Crono, etc. I believe that this has to be the case, or else Crono and Lucca would have no reason to travel back to 600 AD to save Marle.
So, I guess all I'm really saying is that Leene would've been found regardless of anything Crono, Frog or Lucca did. She has to be, else Crono and Lucca would never travel back in time, even though Marle would.