Drupal and WPMU really serve different goals.
WPMU is very specifically designed to provide secure blog hosting with some customization through themes and plugins. How Posts/Pages function is very pre-defined. The site-admin (overall server admin) pre-determines the themes and plugins available to all the sites. Then to create a new blog a user (or the admin) simply types in the new site name. Because the use-case of it being a blog is already known, the site can be deployed and be instantly functional to the user. WPMU is about providing a fairly simple self-service site to end users.
Drupal is designed to be a flexible site-building framework. Unlike WPMU, it doesn't pre-define the functionality of the site. Instead it gives the administrator a blank slate to define the content types such as blog post, news article, pages, etc with very granular control over the fields that make up each content type. A default install includes a blog content type and some basic user roles, but they are more for example than fully functional for deployment. Superficially there are similarities in Themes and Modules, but Modules are more like adding core functionality to develop on top of than wordpress plugins that are typically more drop-in functionality (dunno if I'm explaining that clearly).
Both are very capable systems and which you choose to use really depends on the goal of your site/service. If you are looking to build a blog hosting service, I would definitely recommend WPMU. If you are looking for custom site development for multiple independent sites that may not be blogs, I would look at Drupal (or multiple separate standalone and customized WordPress sites).
The merge of WordPress and WordPress MU is really inconsequential. The real question should be what your site/service goals are.