I can't even scuttle them as the destroy option wants to retire them at the nearest starport, which they can't reach. How do I prevent them from capture by enemy forces? They've got the best endgame tech short of zero-point reactor and I don't want that to reach enemy hands. How to dispose of these stranded and vunerable construction ships? You'd think Scotty could disconnect some equipment to reduce the energy load, but no.... They're adrift.
Best current solution I've come up with is to gift them to a pirate faction that I'm just about to eliminate.
Possible Fix:
It would be nice if construction ships could upgrade other ships in space. If they can build mining stations, why can't they build ships? There should be a refit option on the right-click menu. Select construction ship A, right click on upgradable ship B and the menu should have an option to refit ship B.

