I presume you know enough Python to be able to open these files, read and parse the content and come up with a data structure such as a dict of the name value pairs in the file.
In your own standalone program you can use the DAL by itself from gluon/dal import DAL, Field then you can connect to your database and define your model as per chapter 6 of the book. Look at Chapter 4 first to get a good overview of web2py. The data from the file can be driven into the appropriate table with db.insert(...) Unlike the web applications you need to db.commit() at the end if everything succeeds or db.rollback() if you want to back out, this is done automatically for you in the web request-response cycle. Another option is you could write a normal web app that has a controller that will take the ini file key value pairs as keyword args and then either fire the URL at the origin or a standalone program that reads the ini files and fires the URLs in using urllib2.
