Regarding adding better security options, this is what I propose...
Allow for both the user and pass to be either entered via command line arguments or through the config file. If you enter both the user and pass in either location, it will assume you want the password saved because you entered it in clear text. It will encrypt the pass and save it into a new field in the config file and set the pass to "" in the config file.
If you enter only the user via the command line, the software will assume you want the utmost security and will prompt for you password at application start without displaying the password at any time. In this case the software will not save the password in any way (even encrypted), so you will need to pass the user every time you launch the application and enter your pass at the command prompt.
If you are not super paranoid, you can enter the pass in clear text via the command line and it will be saved in an encrypted format for you. You can then clear your bash_history to remove any traces of the clear text pass and use the application without having to enter a pass again. If you are super paranoid, then you can just enter the user and be prompted for the hidden pass every time you use the application.
That should cover the security concerns. Do you guys agree?