User blog comment:JakePT/Lair of the Shadow Broker is INCREDIBLE/@comment-1900300-20100909110804/@comment-1691295-20100909113008

Still, you're in a Cerberus ship, filled with Cerberus operatives, the Illusive Man probably knows where you are and what you're doing.

Besides, you were never 'in' Cerberus to begin with, and characters say you work for Cerberus is not an unreasonable conclusion given the above, regardless of whether or not you're listening to Cerberus. Not to mention that the emails aren't orders, they're just requests. You're the chump for still doing what he says, but even then there are reasons for doing those missions that don't involve helping Cerberus.

Whether or not you're in Cerberus doesn't affect the fact that he can contact you if he wants and that you're using Cerberus resources.

Nothing in the DLC contradicts the ending. Want characters not to say you work for Cerberus? Stop using the Normandy, fire your crew, ignore messages from the Illusive man and issue a press release noting your allegiances.