The Alliance isn't exactly going to forgive-and-forget Miranda working for the most notorious terrorist organization in Council space.
Speaking of Miranda, it seems she might not be a squad member in ME3, which would be odd considering the emphasis attached to her character in the previous game.
Shepherd at least has the "I'm a Spectre" excuse, and as we can see in the demo even that
seems to have only saved him from summary execution; he's still jailed & awaiting trial...
Well Miranda can join the "good" side by quitting Cerberus at the end of ME2 depending on the choices Shep makes. Also it's known that Cerberus has some level of support within the Alliance military so I'm sure the Alliance would overlook her previous allegiance if it meant stopping the Reapers.