Having just experienced a Fedex (Hackathon) day I can attest to the fact that companies tend to make most of the mistakes highlighted in the article.
One thing that everybody seems to miss is that Hackathons are a great gauge for the wet skills and team dynamics of your staff. Removing all corporate structures and leveling the playing field by forcing people to advocate ideas and follow them through is an awesome HR tool. You can see which members have a natural knack for leading a team and commanding respect and which individuals have good chemistry and work well together.
I'd say there is more value in that than the actual code and ideas (Which normally get ignored by business anyway.)