Sir Ulrich Von Lichenstien wrote...
Erm they did go rogue, either in the end of mission report or in an email after (forgot which) TIM states that he had called for the place to be shutdown just before the riots started. All the doctors involved that survived were dismissed from Cerberus and to all intents and purposes Shep and Jack did Cerberus a favour by blasting the place to kingdom come.
I would call that email and explanation simply a damage-control attempt... and quite a bad one.
TIM basically tries to save face before you and tries to avoid getting you as enemy (or strengthen the negative view of Cerberus from ME1) for something that has happened so long ago.
I would even call out TIM on this email and say it's a big BS.
Black Ops organizations, like Cerberus, conducting extremely illegal researches will include additional reporting structure exactly to avoid cells going rouge.
E.g.: Like a common guard who sees the daily operation and raise the red flag in case something happens. The existence of these additional controls (internal sleeping agents) are treated as a known fact by the cell's leadership and acts as a natural brake before the cell push anything out of the record. If TIM trusts his cell's leadership in such an extent, that's simply stupid... and we know he not that kind of a guy.
On the Normandy2, you have Miranda and Jacob as your obvious watchers. Miranda always writes reports on how the mission is progressing and assessing the situation. The crew is monitored by a professional, Kelly, and someone also reads her reports...
Additionally you have all the non-Alliance-past crew members acting as potential sleeper agents and you have all the listening devices around the ship (as Tali & Morinth mentions).
In ME2 you turn both Miranda and Jacob. You save your crew and they are not in the position to do anything when you become a rouge-Cerberus agent. EDI just takes over the ship and uses it as her new shiny body. All three layers of guarantees TIM had built in fail in one critical moment.
For Miranda, saying during Jack's mission, the operation has gone rouge... is like a 'plausible denial'.
Just watch some TV series out there if you need inspiration how this kind of groups work would go.... or join a Black Ops organization.

(in one of the MMOs out there, like EVE online).
Sir Ulrich Von Lichenstien wrote...
If you take Miranda with you on this mission she does make a comment when one of the play logs has the guy talking about TIM not knowing what they are truly doing stating that they obviously went rogue.
That being said, if you want to take the 'anti-cerberus' line of thought, Miranda pretty much is blinded by loyalty due to all the stuff Cerberus has done for her. So it isn't a case of dumb, it is a case of believing they are doing the right thing.
I agree, Miranda is blinded with her Cerberus loyalty and only starts to have her own moral compass, when you help her with her little problem.
Question:
I don't remember correctly Miranda's loyalty mission's close screen text. What does it say? Does Cerberus know where her sister is moved to?

That can come back and bite in her genetically perfect ass.
If yes and you have decided to blow up the station and showed your middle finger to TIM,

it would mean you have to deal with the situation again in an ME2 DLC or in ME3.
FFFFUUUUU