Okay so, proposed TRON Legacy headcanon time:
The disks were never meant to be permanent.
They are, in essence, debug tools to quickly access and tinker with programs’ code.
It would never make sense for a functioning society of living individuals to have an object as essential to one’s existence be as easily snatchable as they’re presented in Legacy and Uprising. It’s absurd. But it would make sense from a programmer’s point of view, as this whole society is still work-in-progress, not yet ready for its main purpose as a retreat into the digital realm for living human beings.
When you think of the system in Legacy as a digital construction zone, one in which there’s one central central programmer who designs and shapes literally everything around him, having every program’s code as easily accessible and editable as they are suddenly makes a lot more sense.
In this digital realm, these programs need to be debugged, edited, pruned to perfection at a moment’s notice. We see this very thing in action in Legacy when Flynn uses Quorra’s disk to quickly isolate and repair her corrupted code on the light sailer.
So that’s my proposal. In the 1982 movie, the disks were a symbol of slavery under a tyrannical MCP, forced upon each captured program much the way shackles and a weapon would be forced upon a gladiator. In Legacy, they’re the symbol of a powerful but stubborn creator, who’s fingerprints are found in the code of each and every program in the grid.
It shows Flynn’s brilliant yet shortsighted nature that when he looked upon the disks of the original grid, he didn’t see them for their use as shackles, tools of surveillance and slavery, but for their use as diagnostic tools used to touch the soul of each and every program in his grand new utopia.