Indeed - you have thought half the answer for yourself - The blender modules won't be available from outside blender, but you can have a script inside blender to receive data from outside.
The easiest way would be to use XMLRPC - use a script that loads with Blender, and stars a Python XMLRPC server - then you will be able to send commands into that script from outside.
It is easier than it sounds - check the Python documentation for XMLRPC (it will even allow you to have python 2.7 scripts outside blender communicating with the Python 3 that runs inside blender) -
http://docs.python.org/3.3/library/xmlrpc.server.html#module-xmlrpc.server