User blog comment:Hunter Zealot/Tie ins at the Trial/@comment-1221773-20110516005330

Shepard's in the free and clear for anything he/she did in Mass Effect. The Commander was still in charge of the Normandy and flying missions for the Alliance for a month after the end of ME. If the Alliance was going to charge Shepard for any crimes committed in ME, I strongly doubt Shepard would still have been on active duty.

I don't know how it will be for ME2 events, but aside from Arrival, there's little there that could be considered crimes, let alone crimes that the Alliance could charge Shepard with. Maybe the Commander will catch some flak for associating with Cerberus, a known terrorist group, but that's about it. The impression I got from Arrival and ME3 previews is that the trial will be focused primarily on Shepard's actions during Arrival.

And I wouldn't worry about Spectre status too much, the Alliance doesn't have control over that. If Shepard were to actually be convicted I would assume the Citadel Council would revoke it then, but we already know the trial gets interrupted by the Reaper invasion.