A couple seconds later in the movie, the hero is disintegrated by a laser cannon behind his back, scanned and transfered to virtual reality environment where programs break apart when they hit hard things. Suspension of disbelief is a requirement.
OTOH, I am quite surprised Disney got to name its first Tron villain the same as Burroughs mainframe OS. It's worth noting MCP's sidekick name sounds a lot like MARC (the Menu Assisted Resource Control).