Just to throw my $.02 in, this all seems a bit of a "tempest in a teapot".
Sure, exploiting the AIs by selling them so many pretty baubles that they go deep into debt, and can't compete, may seem like a cheesy tactic...until you realize that this is pretty much what the IMF does to Third World nations out here in real life.
Fact is, "tech-whoring", as it's called, is a legitimate technique on all levels of play. The game allows it, and its use is consistent with the game premise.
I've found the GCCG very useful and informative, and appreciate EBZ taking the time and effort to share it with others. While I am more naturally inclined to gigantic games at high difficulty, the GCCG strategy is a lot of fun. And, it lets me play a game quickly, without a lot of micromanagement, when I don't feel like playing a game where I need to wait 5 mins or so each turn for the comp to move my huge numbers of constructors all over the galaxy.
Without GCCG, I probably would play less. And, I think my overall skill at play has benefited from incorporating GCCG tactics.
I also appreciate the efforts Stardock has put into the game. Overall, I think the level of support here on the forums, and the effort that went into making and publishing an enjoyable game has been excellent. (See MOO3 for a lesson on how to make a broken game.)
It's important to remember that, for all of us players, GC is just about having fun and playtime. Of course, for Frogboy et al., it's real-life food on the table. So, I can understand the devs getting a little worked up when it looks like someone has found an endrun around the intended gameplay.
But, in truth, there's no catastrophe here. The "tech-whoring" is not as effective at higher difficulties. The gameplay slips back into the intended path as the difficulty increases, even while using the GCCG methods.
It seems the brunt of the grousing centers around Metaverse scores. The perception is that a few players will slam a huge number of games at low difficulty to get really high Metaverse scores.
Frankly, I don't see much of that. EBZ probably comes the closest to doing this, as would be expected, since he orginated the methodology. But he's not cheating; he's still abiding by the rules of the game and the Metaverse.
I'm not a programmer (Damn it, Jim, I'm a DOCTOR, not a...oh, never mind.), but at least conceptually the solution seems pretty straightforward.
1) Nerf the Metaverse scores a little bit on the lower difficulties. 2) Raise the flag limits on tech and money in the game a bit for low difficulties (to help prevent anomalous scores).
Announce the alteration in Metaverse scoring, so that players who are motivated by Metaverse scores will be encouraged to move up in difficulty (where the AIs can better handle GCCG tactics and gameplay follows a more normal path).
Do not make the new Metaverse scoring retroactive. (When the NFL went from 14 to 16 games per season, they didn't go back and change all the record books.) Any anomalies will be smoothed out over time as new game results continue to be added. Those who racked up big Metaverse scores on low difficulty will have to adapt or lose position.
Making the attempt to prevent hacking and cheating (by using the flag system) is commendable. The Metaverse isn't worth squat if it is hacked. But these anomalous scores at low difficulties are not due to hacking or cheating. They result from legimate tactics, and should be given full credit as legitmate games--only they should, I think, receive fewer Metaverse total points. Since higher tech and money levels can be reached at lower difficulties using legitimate tactics, the trip levels for the red-flags should be raised at these low difficulties.
Hm, this turned out to be a long post for just 2 cents.

But really, I think this whole thing just needs a little tweak, not an overhaul. Now, everyone take a deep breath, and remember that in a few billion years, we're all just a big ball of ice anyway.