@zdenek First, how big is your SD card?
Second, you can probably copy off the config.js file out of the /home/pi/MagicMirror/configure folder and then delete the entire /home/pi/MagicMirror folder. That should give you enough space to get your Pi back up & running.
Third, you can remove the applications that come with the Raspian operating system that aren’t necessary for the Magic Mirror to function with this command:
sudo apt-get remove --purge idle3 java-common libreoffice* minecraft-pi scratch nuscratch penguinspuzzle python-minecraftpi python3-minecraftpi smartsim sonic-pi wolfram-engine
Follow it up with the automated cleanup: sudo apt-get autoremove -y.
That should free up some space once you get your Pi booted again.