There always was a reaction with the Telepod even in the original time-line.
How can you be so sure? If the entity controlled the reaction then in the original timeline there would have been no reaction, since the events hadn't been set in motion yet.
I mean, the Entity controlled the reaction, but it's not really different from anything else, like, for instance, Lucca building Gato, or Gina naming her son "Crono" when he was born. You're speaking about the original time-line in which the Entity didn't do the reaction, we could also imagine a time-line in which Lucca didn't build Gato or one in which Gina named her son "Harry" or something...
We can imagine how the world
was going to be after 1,000AD, before the Entity decided to make Gates, but the fact is that it effectively made Gates anyway. It's like how we could imagine how the world was going to be before Lucca decided to build Gato, the fact is that she effectively built him anyway, so that the "original" future without Gato never existed.
As some scientist from Chronopolis says in Chrono Cross, the world's aspect is only stabilized by the view point of the one who observes it. In Chrono Trigger, Crono's the one who observes the world. And according to him the Dreamstone-Telepod reaction happened and had always happened.
Err... I'm rambling and going a bit off-topic so, what I meant to say was just that the Entity
did its stuff anyway, and we can't really know what happened in the original time-line since Crono "leaves" it (and cast it in the DBT by the way) as soon as Marle is thrown in the first Gate.