bc6d0fa created the issue
Add support for S3 SSE-KMS (see: http://docs.aws.amazon.com/AmazonS3/latest/dev/UsingKMSEncryption.html). This would enable users to input their KMS Key Id, and Cyberduck can send this key id as part of the upload request.
In the context of AWS CLI commands, you can check out this documentation: http://docs.aws.amazon.com/cli/latest/reference/s3api/put-object.html
You can specify the KMS Key Id by using --ssekms-key-id parameter.