I haven't had it affect a game I've been in yet, but yes I do think that's the most unrealistic aspect of the game engine. I think (x) number of seconds should be deducted from the shot/game clock before an offense begins to function, perhaps based on the difference between the point guard's handling rating and the OD of the player guarding him. So a PG being blanketed on defense might take 7-8 seconds to get the ball upcourt and start the offensive set whereas a PG with much better handling could get the ball upcourt in 3-4 seconds.
Either way, I'd like to see examples like the one listed by original poster be phased out of the game engine.