Unfortunately, I don't think that is possible.
There are several alternate solutions to this issue.
What could be possible is the ability to build these bases as a prerequisite to build a wonder in general. It won't upgrade from the base building, but automatically be a separate building altogether (similar to how the forge of the overlord works).
One could set up a special resource that each play starts with that is consumed when building the base. A problem falls on the refunding of resources if you decide not to build the the wonder.
One could forgo the only one per faction requirement of the wonder base and allow anyone to build these buildings in all cities.
I haven't found a clean solution to the 'issue'. You could ask yourself two questions when finding a solution here:
What are you trying to accomplish? And why would accomplishing this improve the gameplay?
An answer to the second of these questions will lead to better solutions, because I don't think it is possible to stop the building of the second piece (I recall trying before unsuccessfully (or with undesired results))
Its a shame that you cannot pass a player ability with a building to prevent the building of these bases a second time.