Crazyphil

It's a bit embarrassing, but in my case the fault was entirely mine. I seemed to have messed around a bit too much with the system. However, maybe this helps someone else with their problem as well.
 
One of the changes I did to my system caused the /lib directory to be replaced by an actual directory instead of a symlink to /usr/lib. As the init.d script is stored in /usr/lib/init, the boot process couldn't find it anymore under the path it expects it to, the kernel panicked.
 
I then removed the directory including all its contents and replaced it with the correct symlink again. Since then, my Cubietruck has been working fine.