As of version 1, the API is public. There are two parts of the API.
1) The consumer side which is basically the side that MSDEPLOY.EXE, our UI, Web Platform Installer, etc. use.
2) The provdier side which allows people to write providers (like dirPath, setAcl, appHostConfig, etc). This is the side that you could extend to write a "remote batch/command execution" provider.
In the next few weeks, some folks will be posting samples to show how to write a provider.
That's a long winded way to say "yes, you'll be able to extend MSDEPLOY to do this, and you can do it today."
(BTW, the team has been considering writing such a provider as you describe)