Idea is to put all colonies with special resourses at the edge of the map. (with min. 8h or so travel time)
This will make colonies harder to maintain but harder to destroy too - like colonies in real world.
Imagine - if somebody start attacking with all his army your colony, that automaticly means his native city, capital is undefended, so you can ask friends or enemies to attack your offender..
Now colonies rarely under attack - cos you always can be attacked back, so not a big fun there now...
This also may introduce small, fast raiding colony armies, witch will run around and kill citizens or smth.
Impementation is also simple - leave some no mans land and do not allow players appear there (at the borders of map), and put all them with -50 happines (?)