They absolutely can protect against that. Teams with player's bird rights can offer more money over a longer period, and go over the cap to re-sign homegrown players.
The real reason this is a problem is because there is no sense of competition anymore. Instead of GS and OKC having 3 years of an awesome rivalry, where Draymond and Durant were sniping at each other, and Curry was going 1v1 for stretches on Westbrook, we get the super friends.
The rivalries of the old NBA are dead. No more Magic/Bird.