Sadly, the only solution I found is to do conquests against them. You can always send some men to destroy their spawned units, but because they take no morale damage, even 5k vs 5k with a martial of 50 is going to leave you with 2.5k soldiers, and that is using only light infantry.
Hopefully if you wipe the undead other realms will join in taking out the undead, but that won't prevent from another undead land appearing in some random place.

Honestly, the undead are probably the most not fun part of the mod. I've had the undead religion somehow proselytizing realms (which is wtf), and just resigning when I saw a small part of India/tibet being under control by the undead and having a whopping 125k+ death stack. Meanwhile, even while being a god, I had only 20k retinues and similar amount of levy, which is definitely not enough.

I found a Genocide mod
https://steamcommunity.com/sharedfiles/filedetails/?id=618463795

It seems to work or at least load but I haven't gotten the opportunity to try it in game.