That's a very simple fix though. Set a minimum level based on overall guild size. If you cross 600M you can't fall below the top tier or two, etc. So, you can't fall down to level 1 or whatever to just pound a newbie guild.
The point is, those in the mega guilds are paying big bucks. It's literally impossible for someone who is a newbie right now to ever catch them. Unlimited cash or not, the stuff you can buy in a given week is still capped, so you can't spend a million bucks week 1 and 'catch up'. It'll still take a year or more. Yet, for all the cash the top 1% spends, they gate them rewards no one else can get that simply furthers their advantage.
If you want to open things up for AB's or challenges, etc. Fine, but then don't gate it at R9 (which they do) where you can't get those toons that high without access to the stuff you need in the first place. The only place someone not in a top guild can really access them is via guild currency in which you still have to be in a guild that can do fairly well at the latest raid, which, again, isn't going to be a new or even mid level guild.