Ezra Klein has the best take on the Rahm story and what it all means. I have been interested in Rahm ever since the Michele Norris gold star incident. My opinion is that Emanuel is a ruthless genius when it comes to gaining power but he seems to have little concern for what he wants to use the power for.
As for the decision to use military tribunals, Glenzilla, Josh Marshall, and Yglesias all say what needs to said. I will add that what I have noticed that President Obama seems to be able to find the exact limit of what is politically possible(in this case closing Gitmo but keeping miltary tribunals) and then doing what is possible but he does not seem to be able to expand what is politically possible. I find this sad because one of the reasons I supported Obama was I thought he would be able to expand what is politically possible.
Tying these threads together, I would say that the disappointment that exists with Obama comes from his being a President who doesn't know what he will uncompromisingly fight for who is served by aides who don't know what they want power for.