I suggest you post your war flag rules on the featured message board. Then start taking notes on repest offenders. Decide who you think is the greatest problem player and remove them.
Explain to your members why they were removed and how important it is that everyone should participate as we all rely on each other to achieve our personal goals.
See what kind of feedback you get from that.
Before the matchmaking of the next war, put another message regarding war flag use. If the problem persists, remove the next greatest problem player.
Eventually your members will see that you are serious and either start participating or realize they’ll be removed.
You will have a difficult time recruiting and retaining new members if they don’t see that you won’t tolerate non-team players.