Well, the simplest explanation is that he's sitting in custody because he doesn't want to be in Hogwarts while Dumbledore scans it for Tom Riddle's soul with the Map, etc. If he doesn't have a particular plot to carry out during the trial, it's easiest to stay in custody then too, until the Aurors choose to release him after the whole matter is considered closed.
If he wanted, he could almost certainly leave, I agree. But why? If this whole thing is his plot, it's going on well enough without him, and on the other hand he possibly can't be officially present at the trial (unless invited by Dumbledore) to rescue it if something goes wrong. OTOH, if it's not his plot, it would still seem to align with his interests - he has more to gain by offering Harry to help rescue Hermione, once Harry has declared the government etc. his enemies, than he does by offering Harry to help sway the trial.
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: