I really have no idea why people insist on using Akeeba Backups when you can just backup your website through a cron in cPanel/WHM (this is much more reliable).
Now let's go back to your question. What you can do is change the ownership and the permissions on the components folder to only allow Apache write access to specific components directories. Having said that, you cannot really do exactly what you want, which is allowing/disallowing access tofor a component access on some specific directories, since components do not technically access directories, it is Apache (the webserver) that does that.