I like this idea, it is simple and it doesn't add too much speculation. Essentially, your causality ends when you reach The End of Time.
The issue is that this leads to the Magus Paradox. Marle vanished either because Leene's rescue was called off or because Frog was supposed to have literally saved Leene at the time Marle vanished.
What about Magus? When his manner of defeat was changed in 600AD thanks to Melchior's reforging of the Masamune in 1000AD, Magus was sent to 12000BC, where he convinced Queen Zeal to banish the Gurus. Melchior was imprisoned on Mt. Woe. If he is imprisoned on Mt. Woe when the Mammon Machine becomes operational inside the Ocean Palace, then he can't be there (or have someone else, like Crono) pierce it with the Ruby Knife. We know that this must happen because the Ruby Knife becomes the Masamune when it interacts with the Mammon Machine and we see the Masamune in 600AD before we see the events of the Ocean Palace in-game.
No Melchior, no Ruby Knife, no Masamune. We know that the Ruby Knife being placed into the Mammon Machine makes it go haywire and disturb Lavos as a result. Lavos appears, banishes the Gurus throughout time, along with Janus. No haywire Mammon Machine, no Lavos appearance, no Janus (young Magus) banishment. Following TTI, this wouldn't effect Prophet Magus, but would subject Janus to Time Bastard at the moment Janus was supposed to have time traveled.
But, going along with your idea: Magus, who has NOT been to The End of Time, would be the problem. His existence wouldn't make sense from the moment he convinced Queen Zeal to imprison Melchior on Mt. Woe, so he should have vanished right then as Marle did when her ancestor's rescue was called off.
Pointing out a problem without offering a solution, however, wouldn't be professional (haha). What if Crono and Co. time traveling to 12,000 BC "corrected" the paradox? 65million BC is obviously before 12000BC, so the Magus Paradox would not affect it. We know that Crono and Co. are offered direct access to 12000BC from 65million BC. We also know that the gates "age" - meaning that if you go from the present to the past and spend 1 hour there, you will find that 1 hour has passed in the present when you return. Finally, we know that by the time we get to 12000BC, Magus already has a foothold there as a trusted Prophet of Queen Zeal. Therefore, we can reasonably assume that Magus did all of his Prophet dirty work while we were messing around with the Reptites in 65million BC.
As I said before, Magus appears, convinces Queen to banish Gurus - leading to: no Melchior, no Ruby Knife, no Masamune, no haywire Mammon Machine, no Lavos disturbance, no sending Janus to 600AD.
But as soon as Crono and Co. appear, having had met Melchior already in 1000AD, their rescue of him becomes guaranteed, which allows Melchior to give Crono the Ruby Knife, and on and on until the Janus-enters-gate event is restored, thus re-justifying Prophet Magus's existence.
To summarize: Marle appears, rescue party for Leene dissolves, Marle vanishes with it, Crono and Lucca appear, rescue the Queen, Marle makes sense again.
Magus appears, rescue party for Melchior is now required but lacking, Magus vanishes. Crono appears, rescue party for Melchior has arrived, Magus makes sense again.
But why would Magus be able to reappear just because Crono and Co. were eventually going to save Melchior? Marle didn't reappear when Crono and Lucca decided to rescue Leene - it doesn't seem to make sense.
Unfortunately, here is where the similarities between the Marle Paradox and the possible Magus Paradox end. Marle's disappearance itself was the motivator for Crono and Lucca to save Leene. If Marle reappears, Lucca assumes the Queen must be fine and they decide to go back home, then Marle disappears again. They decide again to find the Queen, Marle reappears, they decide to go home and then Marle disappears again, and so on and so forth until they figure it out.
Magus would disappear because he suggested Melchior's banishment to Queen Zeal. Crono and Co. would arrive in a world where the Guru's rescue would be an eventuality, given Magus's advice to Queen Zeal that was carried out before our heroes even arrived in 12,000BC. So, there is no bouncing back and forth between results like there is with Marle's situation. Additionally, we know from Marle's example that disappearing due to an apparent paradox does not instantly erase everyone's memories of you (Magus's effect on 12,000BC would be seen by Crono even if Magus forced himself into a paradox just before their arrival and everyone in Zeal Kingdom would remember his presence there.)
And again, we are given direct access to 12000BC from the prehistoric era in the game without needing to travel ahead first to see the results of Magus's horrid miscalculation (Magus and the Gurus time travel event not happening would render much of Crono and Co.'s adventure impossible - which doesn't threaten them at all because they have been to the EoT and, by your idea, have had their causality strings severed.)
TL;DR VERSION:
Zeno's Theory: No TTI before EoT visit.
Possible Problem:
Magus to 12000BC --> Melchior imprisoned, no Ruby Knife in Mammon Machine, no Lavos disturbance, Janus to 600AD interrupted.
If no Janus 600AD travel and Prophet Magus no TTI --> Marle Paradox-like Magus Paradox occurs
Possible Solution:
Magus to 12,000BC at Time X, becomes Prophet Magus and orders Melchior imprisoned at Time X+1, Prophet Magus vanishes
Crono to 12,000BC at Time (X+1) + N, is assumed to eventually free Melchior --> Prophet Magus reinstated