For that you can override their respective Spawn Replacement file via
Data Pack.
The original can be copied from inside the mod file (opened like a ZIP archive) under
"data/pixelmon/spawn_replacement/villager.json" and added into your Data Pack under the same file path. There you can change
"enabled" to
false to deactivate the replacement.
You can find an example that deactivates all replacements here:
https://pixelmonmod.com/viewtopic.php?f=175&t=31343However, keep in mind that removing Pixelmon NPCs will lock you out of some content accessed via Quests.