A few things
A. In order to USE phpMyAmin, you do not need to be able to Write to the config.inc.php file. That file is used for CONFIGURING phpMyAdmin. The phpMyAdmin remote user needs Read access.
B. When you secure phpMyAdmin, usernames and passwords (based on MySQL Rights) will govern what can be done with/in phpMyAdmin.
In my opinion, you should spend some time learning about the Linux OS, the client server model and file permissions. You will need to understand these things to avoid security problems -- such as world-writable configuration files. This is particularly true if you are going to use widely distributed Open Source packages (like phpMyAdmin, WordPress, Joomla, etc). Everyone knows what files are 'where', and how to manipulate them.
If you haven't already, you should probably also learn an SSH (Secure Shell) tool like Tunnelier or Putty,