I actually take a whole new angle to the Marle question in my Chrono Trigger novel, something that will be explained in full in an upcoming chapter.
While the search for the real Queen Lenne being called off is certainly a factor, that is not the reason why Leene is suddenly destined to die and Marle subsequently disappears. What happens is that Marle's sudden appearance in the middle ages throws a wrench into Yakra's plans for the Kingdom. Yakra's plan is to hold the Queen captive for a time while the King (Aldren) makes a complete shambles of things in the attempt to find her. When the situation in Guardia - specifically Truce Province - reaches its most chaotic point, Yakra intends to release Queen Leene to trigger a bitter succession battle for the throne, which would greatly weaken the Kingdom and make it that much easier for the Mystics to win the war. When Marle suddenly shows up, that plan is completely thrown out the window.
The surprising twist is that Yakra believes that the Queen's double is actually another Mystic Lord like himself, and is deliberately trying to sabotage his efforts for his own nefarious purposes. Yakra's greatest fear is that there might be a spy among his followers that would free the real Queen at the same time that the false Queen is in the castle, suddenly exposing the fact that the Mystics can assume human form with their magic, thus putting Yakra himself - in the guise of Chancellor Goran - and his entire operation in great peril. To prevent this situation from coming about, Yakra decides that Queen Leene has to die to cut his losses.
The very moment when Yakra makes this decision is when Marle disappears. His intent is enough to effect reality as far as Marle's existence is concerned, partly because Crono and Lucca (and everyone else) are unaware of what has happened. In fact, the entire future of the year 1000 is effectively erased when Yakra makes his decision. The reason why Crono and Lucca do not disappear with the obliteration of their timeline is because they are destined (or potentially destined) to figure out what has happened to the real Queen Leene and rescue her before she is killed. (I don't use the time-traveler's immunity device here.) But Marle doesn't actually return to existence until the moment when Queen Leene's safety is fully assured. Crono and Lucca's intent is not enough. While this brings up questions of causality and intent, and even predestination, I prefer to present things in a way where the choices of our heroes matter, and that they can actually fail if they make a bad choice or are not skilled enough to survive the dangers they face.
The only part of all this where the "entity" might play a role is in the fact that Marle and Leene are genetically identical (Marle is 16 and Leene is 20, but are otherwise the same) despite not being the same person and not being actual twins. The odds of two members of the same family separated by 400 years looking exactly the same, as Lucca points out, are astronomical; basically impossible.
I don't think any time-traveling plot is 100% solid and unassailable. Temporal mechanics is really tough stuff. All I can do is write an interesting yarn and hope that readers like it enough to continue reading.