So back in the day (July 9 and July 10 precisely), I was having trouble with the wiki not embedding in D2L, having it pop out and not stay in the frameset. What it came down to, and was something I wasn’t 100% sure of at the time, was that the MediaWiki version we were using was fairly old. After attempting two upgrades, we now have a wiki that stays in the box, but IE 7/8 break the login (especially on the deep frozen computers in our labs). That problem is part of the default settings of the browser, where you have to override the privacy settings through Tools > Internet Options > Privacy tab > Advanced > Override Automatic Cookie Handling.
So for now, we’re still having trouble with legacy versions of MediaWiki, but on my personal page, the latest MediaWiki install is great and works fine with most browsers. Thanks again to Barry Dahl for the inspiration to do this.