Regarding the port battles i would implement them only as player-vs-AI battles, something we already have on war server if a neutral port is attacked. The capturing nation (the players) should keep the port for a fixed time, for example for 2 weeks (4 weeks, one month, choose one) and after this time it automatically goes back to neutral during maintenance. Next chance for clans and nations to capture it and this keeps the map dynamically.
tl;dr
* player could capture only neutral ports
* battles only against AI
* ports go neutral again after certain time