So I got it fixed myself and will leave here what worked for me in case other people run into this issue.
***If this is not wanted by the admins you can remove this thread***
To fix it I unmounted all zfs filesystems using zfs unmount -f [zfsmount] and temporarily removed the mountpoints so the point where the pool should be mounted is completely empty.
After that it was possible for me to run the update using apt -f install. Then you only need to recreate the mountpoints and mount the zfs filesystems. I had some problems with mounting the filesystem afterwards but this was gone after a restart.