I just released a new patch that enables achievements for all - v1.0.8
I have decided to remove the achievement disabling "feature" for now. The motivation behind this feature was to make achievements truly count and not be easily obtained through the plethora of ways Crea's modding makes it possible. The blanket disabling of achievements for all mods greatly deters modding which essentially undermines exactly what I was wanting to achieve with Crea from the start - a moddable sandbox game.
I hope that in the future I will come up with a viable method to disable achievements in a mod friendly fashion. For now though, everyone can enjoy mods and if you want to cheat to get achievements then good for you.