I doubt they'd have him arrested for destruction of Ministry property, because it would be such a PR disaster.
Doesn't seem like anything a few lies and coercion of a non-free press couldn't handle.
Or, say, stun him then let a different dementor eat him then show everyone how the delusional fool died trying.
I seriously doubt that if the Boy Who Lived killed a dementor in front of the Wizengamot, their response would be "let's let a dementor eat him to make an example of him." They may not respect him, but these are still people who've been celebrating Harry Potter Day for years.
Just because the members of the Wizengamot are stuck in a hate-spiral with respect to Hermione doesn't mean that they're exceptionally evil people regarding other issues (this is as good a place as any to take note of the chapter title.)
EDIT: New discussion thread here.
This is a new thread to discuss Eliezer Yudkowsky's Harry Potter and the Methods of Rationality and anything related to it. With two chapters recently the previous thread has very quickly reached 500 comments. The latest chapter as of 17th March 2012 is Ch. 79.
There is now a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author's Notes. (This goes up to the notes for chapter 76, and is now not updating. The authors notes from chapter 77 onwards are on hpmor.com.)
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: one, two, three, four, five, six, seven, eight, nine, ten.
As a reminder, it's often useful to start your comment by indicating which chapter you are commenting on.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: