My two cents..
Lets say she dropped it. That would mean that once the portal is open, she gets broken up into peices thanks to the telepod, dropping the amulet before that. Once Crono gets on he *doesn't* drop the amulet. Doesn't that seem like a bit of huge luck that Marle would drop it? Not only that but then Lucca has to make a gate key *without* the amulet, which is true, but up until I read this, I always thought thats how she made the gate key =/
If we say its a higher entity, then Marle didn't drop it and it wasn't broken up into peices because the entity wanted Crono to go through the gate, setting off a chain events. That is what the entity wanted to happen but if I'm not mistaken, its the only time the entity directly influences something like that. It may have done things such as the gates but gates and making Marle drop her amulet are very different, in my view.
I think it is just going with unsatisfactory answers. Perhaps that can be explained in Chrono Trigger + =)
Have a great day everyone.