Would it have been actually legal? Yeah, I know, they all signed a contract, but, there were many international citizens working through The Command. What if the head of state of a country said, you know, Alex, I've been thinking and I really don't want you removing any of my nephew Agent Cuddlebunny's memories now that he's retiring.
And. morally, Who Watches The Watchers? Who ensures that only super secret UNCLE knowledge is removed and makes sure that people aren't reprogrammed to believe a certain way. Cue Rod Serling. Forget The Stepford Wives, how about The Stepford Ex-Agents?
Would there be a level of agent, such as Waverly, or even just the different Sections' CEA whose knowledge would be so essential that the risk of deprogramming wouldn't be worth it?
And, really, the little twirly machine? Come on, it looked like it belonged in a state fair carnival....