If a war is ongoing in a system, a player can easily play for both sides. It's too easy a mechanic to fudge.
I suggestion the player, upon entering a system in (civil) war, is presented with a message from an NPC demanding that they choose sides. The player could choose side A or B, or the player could choose to remain unaligned in the conflict, but unable to participate in the local conflict zones for the rest of the war.
If there are multiple wars ongoing in a system, the player would receive 2 messages.
I suggestion the player, upon entering a system in (civil) war, is presented with a message from an NPC demanding that they choose sides. The player could choose side A or B, or the player could choose to remain unaligned in the conflict, but unable to participate in the local conflict zones for the rest of the war.
If there are multiple wars ongoing in a system, the player would receive 2 messages.