Let's finish this post with the following feedback from the Devs:
We are aware of the problem and will try to come up with a solution soonish. The server is obviously not ready for 2 or more competing guilds. This wasn't such a big issue before with Evo and Prog for whatever reason, example being players weren't able to solo lower tier Raid encounters etc.
Creating instances of said Zones with lockouts would be the best solution really. Im not sure if that is an approach that is technically feasible. Need to check (we gained some knowledge with instances due to LDoN).
As for a current solution, i can only suggest that the 3 guild leaders in question will meet and create a schedule on who can take a shot at which time. And this would include offitimes when people would just go for /ran 100 instead of DKP for some mobs or just the fun of it.
I can create a Leader Only Subforum for Jeido, Rerfu and the current Progeny leader (not sure whos in charge) so you 3 can setup a rotation and communicate with your guilds.
We understand the frustration that this would cause, but atm i cannot think of a different solution then to just respect your peers and their raid goals.