I don't think there's any way to prevent to AI from taking over your territory by building bases close to your borders, but you can mitigate it. One way is to play on larger maps. The AI will, on the average,start further away from you. Another way is to modify Alphax.txt: Find the line

8, ; Territory: max distance from base

and change the 8 to some larger value. For example, if you change the value to 16, then your land borders will extend twice as far. Unfortunately, this change doesn't affect sea borders. I don't know of any way to expand sea borders beyond one tile from your coastal bases. As an extreme measure, you could modify Alphax.txt to disable Sea Colony Pods. Instructions for how to do so, see the following link:

http://apolyton.net/showthread.php/114495-Sea-colony-pods

Finally, I don't know know exactly how units are moved when treaties are ended, but I seem to recall that's it's more complicated than you might think.

Thanks for that information.

It is quite possible none of this has changed from the original game... because this is the first time i have ever had an ally on the same landmass. This is because I do not pursue diplomacy much - their all unreasonable idiots - especially on the same landmass (but being unreasonable idiots is good, because it is more fun wiping them out).

The difference here is that the Pirates allied with me and then a volcano raised one of their cities to join with my landmass. (Which is a very unique situation).

After they broke the alliance and then later on attacked me, i now have a number of useless cities rammed up the ass of my main cities - how do i disband them? (apart from gifting and attacking until their gone).

I know of two ways to disband existing bases:

1. Move a military unit into the base and press the "B" key. This will cause the base to be obliterated, but counts against you as an atrocity.
2. Rush-build Colony Pods in the base until the base reaches size 1. Then build another Colony Pod before the base grows to size 2. You will be presented with the option to abandon the base. Doing so is not an atrocity, but requires more micromanagement. This technique won't work at lower difficulty levels since building a Colony Pod doesn't cause population reduction.

Ah yea, i forgot about the good old colony pod trick! Which also reminds me that i can put workers on empath to speed things along more. They won't build any slower, because there are no resources (The ones they stole from me, i gave back after taking the city) Because actual resources are far less important to the AI when founding cities compared to ramming them up the players ass!

Edit: actually the ocean cities had no resources even when they were owned by the AI