MySQL DB import/export command line in Windows

Depends what you mean by 'from the command line', but you can generate the DDL via the dbms_metadata package (see here for example).

If you want the data as well then you'd then have to roll your own, unless you find a generic script somewhere on the web. Automating the script with dynamic SQL and the data disctionary is certainly possible - it's what SQL*Developer must do ultimtately - it will just need some work to get right, and to handle things like embedded quotes. No quick fix I'm afraid.

I believe phpMyAdmin uses plain SELECTs and INSERTs to import and export the database.

I don't think you will be able to prevent import/export. I don't remember PhpMyAdmin having options to disable those features.