User blog comment:Ironreaper/Did Shepard leave Ceberus./@comment-1878196-20100910002404

No, I said that because we choose to do some missions postgame (which is simply a gameplay option and has nothing to do with the story), missions that can be done midgame, when, evidently, he was with Cerberus, doesn't mean that NOW (after the ending) he is with them. They won't change the whole interface just because someone puts them off.

But more than that, I said the he rather still is with Cerberus, given the Liara DLC which takes end-game decisions into account and still keeps him within the Cerberus network. That was a response to Ironreaper's mentioning of the Paragon option in the SM.

So, yeah, I think he is still with them.