It's a similar system to the NCAA Mega March Madness package, where the game carried locally will be locked out (I like that term from the Tivo forum referring not to your local team, but another game carried locally), while the other games will be viewable in the package.
In the MMM package, DirecTV is supposed to lift the lockout if your local CBS changes games. I figure the NFL will attempt to do the same thing, but DirecTV hasn't handle the basketball thing all that well yet.
You know it's all about money, and who is getting how much of what piece of pie. In the end the viewer is the last consideration. The NFL doesn't want to give up any money from the networks and the affiliates don't want to lose local advertising revenue. The NFL should just give the networks a lower cost and keep the package open with all games to all subs everywhere (unless the local game doesn't sell out, which has it's own issues, but that's another thread!)