As demonstrated by tests/openpgp/delete-keys.scm, there is no way to delete a
secret subkey. If a secret subkey's fingerprint is passed to
--delete-secret-keys, the whole key is deleted instead of merely the subkey.

Similarly, it is not possible to delete a subkey from the command line (though
it is possible to use --edit-keys' delkey command). If a public subkeys
fingerprint is passed to --delete-keys, the whole key is deleted instead.

Compare T2878.