Yes, that's for sure the smartest way to deal with it, if you have such a specific requirement. New filesystems (zfs, btrfs) with their sub-volumes also make that much easier, because they can dispose of subvolumes, and recreate them very fast.

# btrfs subvolume create foobar Create subvolume '/btrfs/foobar'

### now do all kinds of atrocities in this filesystem

# btrfs subvolume delete foobar Delete subvolume '/btrfs/foobar'