There is a dedicated Active Directory authentication mechanism described here:
http://www.dokuwiki.org/auth:ad
It takes a little bit more to set up as you need to review changes to PHP in the adLDAP section as well as in your local DokuWiki configuration. I had to struggle for a while to get it going, but the instructions are all there (I didn't read them correctly and skipped over areas I thought I'd already done previously).