Hard to figure what this will lead to in baseball, but it is an interesting development. Teams that go over their signing bonus allotments can lose draft picks, so it's not like giving Stewart the $5 million he was seeking was much of an option. The same will be true for other teams. It also doesn't make sense to blow out the bank for a baseball prospect the way the NFL does on high draft picks. The bust rate is exponentially higher in baseball.
I personally think we will see more players sign to play in Japan, but I don't think MLB teams will counter with huge contracts to prevent their loss.
Did the Braves err in not signing Carter? I don't think so.