Yes this plugin requires to be run from command line, from a server that has access to both databases. Piwik must be configured on the first database. In other words, it lets you move data out of Piwik into another database.
A solution in your case may be (that’s just an idea) to import your data in a temporary database and set up a Piwik for that database. Then you can use the plugin to migrate the data from the temporary Piwik/temporary database into the real one.
Remember to backup your database before doing that!