You can deploy a package/program that will do just about anything you do locally from the command line. We often run .vbs and .bat files via SCCM.
You can also run just a command line (or a package w/out source files). We have the command "gpupdate.exe /force" set up as a program. Then we can kick off that program when ever necessary.
It might be good to note however, that it may be a better option to schedule a task locally on a server if you need to make sure a script is run at a certain time every day. But, it's all dependent on your needs.