The "no build radius" around Thrall spawns is a great idea, but the radius is currently too small. You can still build close enough to stop the thralls from spawning. On top of that, it does not free up spawns that were already blocked before it was implemented so it's only a partial solution anyway. We need two things done.
1.) Fix the "no build" radius to be equal to the thrall spawning radius. It should be impossible for players to block the spawns.
2.) Demolish all player structures within the new "no build" radius. Give people a week's notice that this will happen and they'll deal with it. Ark has demo'd player structures within areas every time they do a biome update. No one cares or they get over it quickly. Don't be afraid of pissing off players over short-term losses in order to make the game better in the long term.
The thralls are probably the most important mechanic in the game right now. You need them for crafting. You need a dancer to heal corruption so you can go caving. You need priests to summon your god. You need high-priests to be able to change religions. Plus all the lore they offer. Having almost the entire server devoid of thralls really really hurts the overall game. It's an easy fix. Just rip off the band-aid. It has to be done and the sooner you do it, the less painful it will be.
Let me give you one more option if you want to be more fair. Do a full item and structure wipe, reset engrams again, but keep player level progression and XP. Again, Ark did this just a month or so after release and no one cared. Most players would welcome it to get rid of all the abandoned buildings. Plus, everyone has that one spot that they wish they could build on. Unless the decay system is very close to being ready, then a structure wipe must happen eventually anyway. Again, the sooner it happens, the less painful it will be.
Concentrate on the long-term health of the game and don't worry about hurting player's feelings about losing their base or whatever. You don't need to have a "no wipe" policy to get people to play the game. Most people are fine with wipes when it's necessary. It's the early days of early access. They'll get over it if it makes the game better.