Clean URLs with multi-site only with suffixes / sub-folders
think you will require a separate virtualhost entry for each of the sub-sites.  That should direct visitors to the correct location and negate any need for redirection.

At the moment you're using aliases to effectively send all traffic to the same place, I think using virtualhosts will separate the traffic a bit better and help you turn on clean URLs.

I'm going to assume your core Drupal files are at /var/www/html.


You definitely need to read the documentation in /var/www/html/sites/sites.php and set that up if you haven't already.
You do need to set the $basepath in each site's settings.php
In Apache it kind of depends what OS you're using but you basically want to turn on NameVirtualHost in Apache and then tell it where to send visitors:

Here's how to do it in Ubuntu
Here's how to do it in CentOS which probably also translates to RHEL/Fedora



Those links give the full setup, so you've probably already done the first few steps.  Keep going down the page to find the Virtual Host section.

Finally, clean URLs need to be enabled in each of your sites, one by one.