I always liked the concept of the Tower of Zot, a tower hidden in the sky (as evidenced by FFIV:DS and Amano's original illustrations), ruled by a powerful being of the air that only if one knew where it was located in the sky, could be accessed.
As for its execution in FFIV... it did feel a bit cheap that they took the approach they did.
I honestly don't think the Clerics had any idea what was going on. The flow of events seem to be this...
(Not actually said, but they seem to act as if Cecil is asking for the crystal) "Cecil: Can I borrow the Earth Crystal?" "Cleric: If you can get it back from the Dark Elf, sure. Favor for a favor."
Then...
"Clerics: You got the crystal back!" (Dark booming voice from above rings out) "Kain: Well done; Cecil, I will take you to where Rosa is."
"Clerics: Seems you have some situation of your own. You can Borrow the Crystal, but make sure to return it!"
(Cecil never gets back to them)
This may somewhat explain why Troia in particular is the most suspicious of Cecil in The After Years since he blatantly breaks his promise and only ever gets them back the Earth Crystal when the entire situation is said and done.
Your approach to make the Crystal itself a warping point (or start an automatic sequence of events) where Cecil resolves to trade the Earth Crystal for Rosa and only then Kain is called and the Tower of Zot entrance is a one way trip, I could see that working well within the context.