Yes, this can be done. One approach is to invoke Lotus Notes from COM. You could have a file called Test.vbs with lines like the following:
Dim session, db, agent
Set session = CreateObject("Lotus.NotesSession")
Set db = session.Getdatabase("", "agenttest.nsf", false)
Set agent = db.Getagent("hello world")
If the agent produces output it will be written to log.nsf
You can invoke the VBS file from a batch file using the CScript.exe command e.g.
Another approach you can take is to invoke an agent from a browser e.g. http://server/db.nsf/SomeAgent?OpenAgent