This feature is being implemented in the upcoming version of Akeeba Backup for WordPress. I am trying to release it today or, if I don't make it, tomorrow morning (GMT+3 timezone, I guess I am 6 to 8 hours ahead of your timezone?).
If you are using the multisite feature included with WordPress itself you will be able to backup and restore WordPress Multisite sites without the need to do anything special. If you are using third party plugins which distribute the multisite databases to different MySQL databases and/or mess around with the domain names, unfortunately we can't help much :( These plugins tend to store their configuration in various odd places, meaning that you'll have to do the reconfiguration of the restored site manually (unless, of course, you are restoring to the exact same server and user account you backed up from).
When you will be restoring the site you will be asked for the URLs of each one of the multisites. This is required for us to reconfigure them and fix the links inside each multisite. You have to make sure that whatever you're using there resolves on the new server. Again, this only makes a difference if you are not restoring to the same server and/or user account as the one you backed up from.
So, just a few more hours of patience :)
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!