How do I remove many system roots from Apple System Keychain?
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