Setting Up CiviCRM Multisite on Wordpress
It should be vastly superior to run multisite for the very fact you state: "That way people who register for the site will be added to our main Civi user database, rather than keeping track of two separate databases on each website." 

One of the main benefits of using a CRM is to have a centralized database of all constituent information, be it contacts, contributions, events, etc. If you split it up, you are only causing yourself headaches later on trying to merge it.

Getting multisite working is worth it.  (Note: I haven't an idea how well Wordpress does multisite; my experience is usign Drupal.)