For the most part, the plug-in is just calling scripts in the <sdk>/bin folder. You should be able to manually call them from the command line to bypass Eclipse.
Compile: monkeyc (self documenting) Run Simulator: connectiq Push to Simulator: monkeydo <prg file to push>
The current package tool is not particularly command line friendly so I would recommend using the plug-in to package your app for the time being. The next release will deprecate the package tool and add an option to the compiler to package a project.
That script is set up to work with the packager, but as Ken said, the package tool isn't really command line friendly, so the script doesn't exactly work just yet with the packager. And as of yet, there is nothing for automated deployment.
