He may leave briefly for the trial, but unless a move is made at that precise moment, in general I think he's going to hunker down inside his fortress of Hogwarts, defend it more tightly, and search it for Voldemort's soul more thoroughly.
The whole trial can't have been set up just to get him out for a few hours; there must be other important Wizengamot votes that he as Chief Warlock (and important political figure) must attend. He must leave Hogwarts regularaly for a few hours at a time for that reason.
On the other hand, he may routinely loop back with his Time Turner to cover up these absences, including Hermione's trial, so that there is always a Dumbledore in Hogwarts...
I'm thinking more about him having to leave if Harry raises a ruckus somewhere. Like the Azkaban breakout.
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: