Together, we are the United Nations
Gunulfr ok Øgotr ok Aslakr ok Rolfr resþu sten þænsi æftir Ful, felaga sin, ær warþ ... døþr, þa kunungar barþusk.
When a fort is destroyed, is it forever controlled by the enemy that destroyed it?
No. It just becomes a regular space with whatever terrain is in there.
If not, does that mean every destroyed fort should have both a destroyed marker and a control token?
If that's the case, how are you guys marking control with the limited amount of them?
It's not the destroyed forts that are going to be your main issue ...
Usually in FTF play, only ambiguities in the frontline are marked with control markers. It is understood by the players that everything behind that line is controlled by the player behind whose front the spaces are.
Of course, in online play you can have unlimited markers