It would actually be easier without GC affiliations ... in theory.
Currently, to fix a match you first have to organize two parties from two different GC's, which means you need a somewhat even split of GC affiliates. Second, you need to fill the exact amount of players to actually get a queue to go through. Full Pre-mades are often a no-go, because the number random queued solo-players can generate a dead queue line. The game has conniption fits when it tries to fill a full match with uneven sets of players. Third, the two independent parties from two different GC's need to get into the same match for them to fix it. It's possible to organize that kind of thing with 3rd party chat, such as discord, but it is still a headache, and you can only skip 3 queues before it's a ban. This doesn't seem like much; however, one, rather massive, drawback to match-fixers is that not all of the three GC's queue equally. Mael has astronomically long queues, whereas Adders are relatively short. This means that it may actually be impossible for your two pre-made parties to get into the same match, depending on how many people are queuing for each GC at that time. The fact that queues are naturally long due to GC restrictions just makes this issue worse. Finally, if you manage all of the above and get into a match, you still have to deal with the logistics of random players. In a full 72 man game, you have 2 other alliances that can throw a wrench into your match fixing efforts. In an incomplete 8-man party, any randoms you have can also make a difference. It's still possible, of course, and one full team of sleeper agents can do a lot of damage, but it is not necessarily easy or effective.
Now, take out GC requirements. The first, and biggest, hurdle to match fixing is completely removed, because anyone can join in your pre-made parties. The queue will also be standardized across all players. There won't be any more discrepancies between Mael / Adder / Flame queues, because you are not required to queue up as any of the 3. That means a far faster queue rate on a "first come, first served" basis. In theory, 2 pre-made parties queuing up at the same time will be FAR more likely to meet each other in the same match under those conditions, because they queued at the same time and neither group are shackled by their traditional GC restriction (ie: Mael has to wait an eternity, whereas Adders can just go right in). The only thing that would be left to throw a wrench into the works is the random players, but how much or little they get in the way will depend on how many solo-players are queuing up at any given time. Peak times vs dead times can still be worked around.
In the end, the only way to stop match fixing completely would be to simply do away with 3-way matches, depending on the game mode. It can be worked into certain things just fine, and there is some fun to be had in that uneven styled game play, but in something like CTF it would only make a mess of what could be a fun and competitive game.