There is no reason that the composition penned by Wolfgang Amadeus Mozart and Antonio Salieri (as well as a third, seemingly unknown composer named Cornetti) should not have been played. Though the piece was only four minutes long, it's rare to hear "new" work from artists so long dead, and it would have been a great shame if we'd been denied the joy of hearing it.
I really see no point in even making this a major concern. It seemed as if it wasn't a real big deal to those involved so I don't understand what the issue would be. I say let them play it in Prague or wherever they choose to play the composition.
Since the lost composition was found in the archives of the Czech Museum of Music and acquried by that museum and presumably stored there for some time, it was appropriate that it was played in Prague. It would also have been appropriate to play the composition in Vienna or Salzburg.
The lost composition of Mozart and Salieri should have been played in Prague. Music is an art, which composers create to be shared. If a lost peice of music were to be found and not shared, the composer's work would have been in vain. By performing the new piece, musicians also gained an opportunity to expand their repertoire.