How do I remove many system roots from Apple System Keychain? The Apple keychain application will not let you remove system roots, it will only allow you to disable them. It will only allow you to disable them one at a time. For each one, you need to go through 3 UI panels and type your password. Is there a way to either automate this or do it all at once? I do not like Apple's current selection of system roots.
Backup keychain before trying anything.

Listing root certificates:

sudo security dump-keychain /System/Library/Keychains/SystemRootCertificates.keychain


Just look in a dump for a names or SHA-1 hash values of certificates that you want to get rid of and write them down.

Now you can delete that root certificates using security delete-certificate command. 


  Usage: delete-certificate [-c name] [-Z hash] [-t] [keychain...]

-c  Specify certificate to delete by its common name
-Z  Specify certificate to delete by its SHA-1 hash value
-t  Also delete user trust settings for this certificate The certificate to be deleted must be uniquely specified either by a

  
  string found in its common name, or by its SHA-1 hash. If no keychains
  are specified to search, the default search list is used.


For example you can delete chinese root certificates using this command: 

sudo security delete-certificate -Z 8BAF4C9B1DF02A92F7DA128EB91BACF498604B6F /System/Library/Keychains/SystemRootCertificates.keychain