I think the real problem with Peter's parents being spies is that it takes away from his everyman origins if it turns out he's the son of special super-agents and heroes and so on. That was a bigger problem in Ultimate Marvel where Peter's Dad is this genius scientist. Fundamentally, Peter's parents are not important to the story and it's a kind of dead end. At the same time, Peter's parents are written by Stan Lee himself in the Lee-Romita era in Annual 5 so it's as canon as they come.
Speaking of Untold Tales...Peter David announced a new story called Symbiote Spider-Man set in the period where Peter wore the Alien Costume but before he got rid of the symbiote...so that's very much in the spirit of the Untold Tales and Spider-Man: Blue.