So I accidently discovered this tonight. It's smart use of the 1 hour limit timer.
Kill 1 easy to get to boss (for example KBD) around 30 minutes before going to a better boss (for example Vindicta) with clannies. This will start the 1 hour timer (during which you can get 1k Marks of War).
Then, 30 minutes later, go to the boss you planned to go to with clannies. You'll easily get 1k Marks of War in the remaining 30 minutes of this same 1 hour timer.
While the instance is still alive for 30 more minutes, your timer has now reset and you can earn 1k Marks of War again.