This isn't a big surprise. I called something
like this happening awhile ago. Maybe I even influenced Bioware? (Ego Trip Woo!) Blame me if you want.

Anyways I don't think you'll be working directly for the Alliance. You'll simply be
working with the Alliance. Which if you really want to save Earth is something you're going to have to do. And Cerberus doesn't have actual Fleets or Armies, so their usefulness is largely at an end. I don't think anyone is going to have the audacity to try and give Shepard orders on what to do once the Reapers show up. Pretty sure it'll be Shepard calling the shots. So I'm not sure what the big deal is for some people.
Basically the Alliance will be like "ZOMG teh Reapers are real!!11 Plz save us Shepard! Here take these shiny new guns we made!"
Besides Cerberus has always been intended to be the "bad guys".
The Alliance is far from being pure sure, but the difference is the Alliance actually serves the interests of humanity. Cerberus more or less just serves
one man's interests. Not really sure why anyone would support a wannabe Dictator. That's what T.I.M. is seriously. All Shepard is to T.I.M. is a popular Hero to be exploited in his rise to Galactic dominance. So why would any Shepard want to be used as tool?
Also to be frank Shepard never really left the Alliance. Never does Shepard go up to anyone and say "I quit! I hate the Alliance!". I mean for crying out loud the guy is still wearing his
N7 Armor. If Shepard doesn't like being Marine why is this still their armor of choice? Obviously Shepard takes a lot of pride in being a Marine, in being an
Alliance Soldier. Shepard may not be happy with what the Alliance has done, but ultimately Shepard knows they have a duty to the Alliance.
Trying to go AWOL is bad idea anyways. Since that would mean the entire Earth military would have orders to either arrest or kill you. Not real helpful if you're trying to save the Galaxy. It's in Shepard's best interests to work with them over Cerberus.
Also remember...
-The Alliance trained Shepard
-The Alliance helped Shepard become the first Human Spectre
-The Alliance has always covered for Shepard's actions in the past