Drupal is free, but I have no experience with connecting it to Windows Active Directory. However, I know it has been at least mentioned, I've just not paid much attention to it.
Here is an article on the topic in case you want to get some information. It's from 2010, so not terribly old, but not absolutely the latest information. I think the plan/path discussed is based on Drupal 6 which is not the latest version. Drupal 7 is possibly best to use right now, and they are at least in the initial stages of designing/building Drupal 8 at this point.
Anwyway, give it a look if you like:
Otherwise, SharePoint is always a good choice, it seems, for enterprise setups, particularly if you want to integrate with existing Microsoft software - it's designed just for that. I have no idea on the costs, but I'm sure it aint cheap.
Drupal is free, but you have to know it or be ready to tackle the learning curve.. or pay a developer who already knows it.
"But thanks be to God, which giveth us the victory through our Lord Jesus Christ." 1 Corinthians 15:57