It was stated in the novelization and hinted in the script that Programs have some vestigial memories and emotional patterns from their Users. Also, the closest we get to an explanation of why the Programs are what they are is Gibbs's line about "our spirit remains in every program we design." Gibbs may have meant it metaphorically, but the in-universe explanation is probably very literal. It also makes for an Accidental Aesop. Technology is only as good or bad as the people who build it. Good people, like Alan, Roy, and Gibbs? Their Programs are User friendly. Someone like Dillinger who isn't as ethical? Well, we get a power-hungry jerk like Sark. And in the case of Flynn? Well, we see his best traits (optimism, determination, clever thinking) in Clu 1.0 and his dark side (ambition, tendency to abuse his friends, need for the crowd's adoration) with Clu 2.0.
If video games are horrifying Blood Sport on the other side of the screen (explicitly shown in the Novelization), then Flynn continuing to run the arcade after seeing what he did in the virtual world would be cruel at the very least and a huge case of God Is Evil at worst. We'd better hope that arcade games are more or less like Wreck-It Ralph, where no one actually was supposed to get hurt; Master Control was just perverting the whole setup anyway, by having non-videogame programs (e.g. accounting programs) fight in gladiatorial duels.
In reality, players are controlling automatons and avatars and fighting against same — or did you really think Pac-Man was chomping actual Ghosts in the game?
Tron is a firewall, even though the term had never been used before. In fact, few companies in 1982 had anything like a firewall, save a simple password protect.
When Flynn repairs the Recognizer, it makes perfect sense, since he wrote Space Paranoids. He probably is the only User who could repair one, at least so quickly, because he is familiar with the code!
The religious parallels between "programs-users" and "humans-gods". Not just the parts where Flynn is basically a Christ figure for the computer world, but the whole fact that not only are most programs not entirely sure if users even exist, but the users aren't even aware that they have created these intelligent beings in their computers. Take this setup a step up into the real world (the novelization takes a few more steps in this direction than the film), and you basically have real-world Deism - the reason we don't see God(s) is because they don't even realize we're here, or self-aware!
Minor one, but whenever a program or a user in the guise of a program expresses extreme emotions, their Tron Lines light up intensely. The big example, being Tron's Big "NO!" causing his blue lines to glow brighter. The same effect happens whenever a program consumes energy from a pure source or is close to dying. Much like how us humans get tired if we are angry or upset, a program's emotional state is burning energy faster the more intense it is.
Adding to the overt religious subtext, the TRON theme features heavy use of a church organ.
When they're digitizing the orange, the lower right hand side of the screen reads "ROM Yori, LOAD Yori"), establishing she pretty much runs the laser. This is why she was captured and turned into a drone instead of being sent to The Games like her husband - Master Control needed her alive. Even with an urgent call from his deity on the line, Tron goes and finds her first, because her role makes her important (beyond his romantic attachment to her). Yori's providing the hideout, she's adept at sabotage (highly illegal power reroute), she's the one who actually makes the plans on how to get into the I/O Tower. It's her connection to Dumont that gets the old Guardian to relent. And she is the one who designed and piloted the getaway vehicle (the Solar Sailer). The only thing she isn't handling is the combat, which is her husband's job.
One would wonder why Dillinger was stupid enough to keep incriminating evidence of his stealing Flynn's game designs and programs. He didn't. The MCP kept them as blackmail; one scene has MCP threatening to publish the evidence on the front page of the New York Times, hinting that the MCP had been blackmailing Dillinger for years.
Why was Tron's disc able to shatter Sark's when most cases of disc combat have Like Cannot Cut Like? Well, first, that upgrade from Alan turned the disc into a Holy Hand Grenade, capable of destroying a full-blown AI. Secondly, Sark was implied to be Dillinger's Program, and Dillinger, while a sneaky and posturing corporate type, wasn't actually very good at programming (he had to steal Flynn's creations instead of succeeding on his own).
When the MCP derezzes, he is revealed to have been created not by Dillinger but by Gibbs. He became what he was because Dillinger corrupted someone else's work, the same way he rose to prominence in the company with Flynn's work.