This shouldn't be especially difficult. Wordpress came up with a rather crude but effective solution for storage of different sites.
If the main sites files are located at wp-content/upload, site two is located at wp-content/sites/2/upload.
As for database data, it's separated into wp_2_exampletable
Flarum could likely follow this pattern since it stores data in much of the same way.
With the help of some admin section to manage this + some form of domain mapping, this could be quite the useful extension.
Originally I had multiple wordpress installs but after switching to multisite, everything became a lot more manageable. I'm not providing hosting, but it makes dealing with completely separate sites much easier.
Now - flarum is in it's very first beta and this is a idea that deserves attention when even the initial install should be considered at least stable.