How about this:
When a city falls from realm control whilst there are rogue troops present, have a possibility that it will turn into a citadel of the undead. It will be harder to regain it, as the undead would even use the walls of the city (but would not repair them). The city would also then become a hotspot for spawning. Though perhaps the undead from the city would generally not wander all that far from their home. Maybe the same for the towns.
The point? Making it more challenging to regain lost cities. Because PvE can be fun and a source of RP history too, especially in the absence of PvP wars.
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As for the idea of tying spawn rates to war activity: it could be something that does not have a certain definite threshold. It would not be an "on/off" switch. Instead having your realm involved in PvP battles would reduce the likelihood of a spawn hotspot forming inside your realm. So, some would game the system and make mock wars. So what? They might always escalate, and beat the stuffing out of just waiting for something to happen. And you would never get a message indicating the effect of your battles on the spawn chance.
Yes, it could then happen that in the middle of a really exciting war with lots of battles there might still be a hotspot forming inside your realm that would totally ruin the war for you. Or, despite a long time of peace, there might not be any hotspots in your realm at all. It could happen, but it beats it being totally random.