Late answer but perhaps someone finds it useful.
I was having quite the same issue. My application runs in OSGi but I have external interfaces that I need to comply with which implies reading the command line arguments.
The key to this is something defined in the new OSGi specification 4.2, namely Framework Launching. You can read about it in the Draft spec (found under Draft on www.osgi.org) in the Life Cycle Layer section.
It's a standard way of launching an OSGi framework (any implementation that supports OSGi 4.2) from a stand-alone java application. The nifty thing is that you don't need to know which implementation you start (Felix, Equinox, ...) as long as it is found in the CLASSPATH.
This way, the your launcher application reads command line arguments, instantiates and starts an OSGi framework and pass the arguments to your bundle (any way you want). What you get in the launcher application is a Context to the framework from which you can communicate with your bundles.
As of Equinox 3.5M6 (I think, well at least M6) this is supported. The latest version of Apache Felix does also support this.