And the answer is: If the creators of Godzilla wanted it to be able to beat Knightmare Frames, then it would beat them, whether you agree with it or not. That is, if they decided to make an episode that would include said Code Geass stuff.
Now, if Godzilla and Knightmare Frames were real, then the result would be unquestionable. But since they're not real, anybody can pretty much believe whatever they like.
The first part of your post makes it sound like I think Knightmare Frames should beat Godzilla (I don't).
Unfortunately, uber-hardcore Trekkies that make Star Trek their religion (they exist, I'm not joking), think that the Federation can beat the Empire.
And not because "quantifiable event x has shown the Federation has significant military advantages over the Empire", but because "the Federation has Quantum Torpedoes, while the Empire has Turbolasers, and lasers won't even penetrate the navigational deflectors of a starship!"
Note that the second statement is actually something that uber-Trekkies have used before. And it also has two logic fallacies in it:
1) "Style over Substance"; that is to say, 'it sounds/looks cooler, so it must be better'. Refer to StarDestroyer.net to see the truth (the site is rather tongue-in-cheek, as it has an Imperial propoganda bent to some pages).
2) "No Limits Fallacy". It is true that in a Star Trek:The Next Generation episode, one of the crewmembers of the 'famous' Enterprise remarks "lasers won't even penetrate our navigational deflectors", when the Enterprise is confronted by some laser-armed spaceships.
The fallacy is in going from "immune to the lasers mounted on x warship" to "immune to all lasers, regardless of laser power". Rather obviously, such a statement is idiocy.
Ironically, a laser capable of unleashing 700 megatons can impart enough momentum to do kinetic damage, so even if a navigational deflector of a Federation starship was immune to lasers irrespective of power, then a 700 megaton laser cannon would still kill a Feddie starship.
The second statement also shows the irrational idea of "turbolaser=laser". In all the Star Wars movies, turbolasers do not behave like laser weapons of any kind. A laser weapon in vacuum would have no visible beam (you'd see a flash at the laser cannon bore/muzzle, and a flash on the target, and even then, the muzzle flash would depend on wavelength; an infrared or ultraviolet laser would have no human-visible muzzle flash), and lasers are lightspeed weapons (which SW turbolasers aren't).
And I only now realize that I've gone completely off-topic/-tangent.