Yes, it is. You’re not supposed to replace system directories with symbolic links.
Well, instead of using symbolic links, you could just as easily mount another filesystem to those directories — the filesystem where you moved their contents to. And if they’re both pointing at the same filesystem, then you can use bind-mounts on the directories that contain the actual files.
Of course, you’ll need to make sure that you’ve properly moved everything over before doing that, and it is actually best done from the live USB/DVD/CD session, so that nothing under the /usr hierarchy of your installed system will be in use.
You don’t even need to chroot for that. Just make sure all of the files are properly moved over to where you want them to be, and then set up bind-mounts in /etc/fstab. See… 
man mount
man fstab
You may also want to check out these two tutorials below…
It’s not the packages doing that. The packages themselves will be perfectly happy with the designated target being a symbolic link. However, it’s the filesystem package that does this.
filesystem makes sure that all of the required directories of the filesystem tree are created, and that they have the proper permissions. And if a directory has been replaced by a symbolic link, it will replace that symbolic link again by a proper directory. 
Show us the output of df. And by the way, you’ve got stuff in your root directory that doesn’t belong there. There should be no hidden files or hidden directories in your root directory (/).