There have been bans of missile weapons in the past, but I don't find any indication that there was any particular action against the gastraphetes.
There is indication of a Greek ban on the use of bows during the Lelantine War
During the the Lelantine War that took place between them it is stated that the two city-states made an agreement banning the use of 'missile weapons'. If this prohibition of a specific type of weapon is true it stands unique and would be the earliest example of arms limitation in history.
- above from: ancientgreekbattles.net
The problem with respect to the Gastraphetes is that this ban and war occurred about 300 years before its invention. (Note that this ban, and indeed the entire battle, has been considered by some to be fictional.)
One other ban which did include both bows and crossbows, was enacted by the Second Council of the Lateran, in 1139. Once again, however, not really relevant to the Gastraphetes.