How Can I Safely Remove WP-Super Cache without messing my site up? [closed]

Besides deactivating and deleting the Plugin, you have to check a few files and folders to be sure everything works.

Perform a full backup

This should go without saying, save all the data you get for eventual troubleshooting.

wp-config.php

Check for the constants WPCACHEHOME and WP_CACHE, and delete/comment them out. Remember where your WPCACHEHOME was located.

Cache-Folder

Delete the folder specified in WPCACHEHOME, using your CPanel or a FTP connection.

Usually this folder is located in wp-content/cache.

Configuration Files

Check your wp-content folder for files like wp-cache-config.php, and rename/delete them.

Test your site

Thoroughly test if everything works as expected.

Plan B

Create a Mirror WordPress installation, and install everything besides the caching plugin. This may be a bit more work, but you do not have to worry about leftovers and broken connections.