I've said it before and I'll say it again; my sole survivor femShep would *never* work for Cerberus and I hated how they railroaded you in ME2 without ever giving you the opportunity to object. I'm convinced she's been indoctrinated by Reaper elevator music or something.
I'd say the same for all but one of my Sheps. One of them wouldn't have even got to Freedom's Progress as they'd have stolen the shuttle and made a run for the closest alliance base before it got that far.
The Shep I just finished last night could conceivably work with Cerberus though. Didn't do any of the Cerberus related missions in ME1, was pro terra-firma and got rid of almost all of the alien team members in 2 without losing a single human. (Losing Tali was probably the most difficult).
It wasn't a particularly pleasant playthrough, but I'm curious as to how that one will play through in 3.