User blog comment:JakePT/Lair of the Shadow Broker is INCREDIBLE/@comment-1900300-20100909110804/@comment-217683-20100909112259

Yes, leaving is ambiguous. After all, hanging up on someone in a rude manner and saying rude things to them does not constitute leaving their employ. This should go without saying, as it was possible to hang up on the Citadel Council in a very rude manner several times in the first game, and to say far worse things than politely telling them to go screw themselves. You can flat-out tell the turian Councilor that, given the chance, you'd happily wipe his entire species off the face of the galaxy! And does any of that constitute leaving? Nope. Even after hanging up on them rudely several times and saying rude things to them, Shepard is still in the employ of the Citadel Council's Office of Special Tactics and Reconnaissance.

So yeah, JakePT is correct that Shepard doesn't actually leave Cerberus. Rude hang-ups and snide comments don't count as leaving.