This is where the mango import/export feature really shines (well, this and mass point creation). Taking the time to create backups by exporting all your configuration (data sources, points, point hierarchies, users, etc, etc) by exporting all and saving the JSON would save you heaps of space. Maybe set a cron job asking a user to save the full export? This will exist as a feature of our next release, automatically saving the export to a text file.
More to your question, if you're operating Mango on a derby database (the default is an embedded derby database), you might be able to backup your mango as you described, but I don't know if it's a good idea. I would think backing up the folder while mango runs would eventually degrade your database if you find yourself doing restores regularly or you have a particularly active database, but that's somewhat speculation. Really, you should just stop the database connections (or Mango entirely) to perform a backup of the folder.
Backing up the folder has the benefits of 1) backing up any DGLux dashboards you create, 2. backing up your personal file additions to graphic views, 3. backing up scripts (these are also backed up in the export, though). If you don't need to back up the first two (and you're using derby), you should be fine to stop your database connections and back up only the /mango directory/madb folder.
If you're running on an SQL database that isn't on the Mango computer, your configuration of datasources, datapoints, etc. is in that database, not the Mango folder.
As far as writing it into a system script, if you've configured Mango as a service you should be able to write "service mango start" and "service mango stop" in your bash.