I'd say beak rubbing is okay... to a point. You'll know it if it starts feeling a bit too... vigorous and intense. At that point, you know he needs a moment to compose himself. And if he's regurgitating for you, yes, you might want to let him cool foo for a minute.
Here's the important thing, though. This is just a natural behavior, not to be confused, on his part, with a "bad" behavior. As such, you don't want your reaction to this to resemble, say, a timeout given for biting or flying to a place that has been deemed off-limits. Personally, I differentiated the two by placing my ekkies on a nearby tree stand or something when they got too worked up. Never back to the cage. This, of course, was a bit more of a challenge with Jolly since he is comfortable with flying and Maya only does so if she suspects impending death. But even so, I would put him on his tree stand and, whenever his stay put conditioning would falter, I would simply keep putting him back until he calmed down.
Another way to deal with it is diversion. Simply channel that raunchy energy into some flight drills, targeting, or any other kind of vigorous training. A tired bird is rarely an amorous one.
