Ok one more suggestion that is simpler.

On 5 realm servers

every city gives max bonus. SO each level 3 city gives 100% rep etc.
there would be 6 of every city level 3-6
there would be 2 level 7 and 8 cities

You can hold as many cities as you want, but the buffs are not stackable
All cities can be attacked cross realm

This would allow the top 5 guilds to still try and hold the same buffs they already have. Give an extra city for smaller guilds to fight over, allow for cross realm war fare to try and hurt your rivals while not getting a bonus for yourself making it harder for other guilds to beat one uber guild. Lets the first guild to level 7 and 8 own both of those cities forcing the second guild to fight them for it. I think this would add competition without causing massive chaos among the players. It keeps the status quo at first, and allows for the ability to maintain the status quo in the long run, while adding some new elements to the mix.