Since Integration Services packages are merely XML files, you can copy them to the destination server manually or by using a script. When using this method, you will have to explicitly copy the dependency files as well on the destination server. Once the packages are copied to the destination server, you can schedule to execute them using SQL agent or any other utility.
Since in this method you will be copying the Integration Services packages on to a File System, the packages can be encrypted using the Package Protection Level property as well as by controlling access to the package and the dependent files(configuration files, checkpoint files, log files etc) by using folder/file permissions at the operating system level.
Please note that the Package Protection Level does NOT protect files that are stored outside the Integration Services package. For example configuration files, checkpoint files, log files will not be protected by the package protection level, so you will have to secure them using some other means such as folder/file permissions at the operating system level.