Ieldra2, I apologize. Just before you commented, I was discussing meta with someone really intend on striking at TIM and at me personally, and then you switched to roleplaying.
The premise wasn't Cerberus - it was me, and my flawed personality. The premise was that I'm "hypocritical" for not wanting to slaughter my only ally in the final game of the series, while I was fine with not working together with a hostile neutral in the middle game of the series. I saw absolutely no similarities between those situations, so you got steamrollered together with that person because I don't have the brakes.

The very reason why I don't get involved into discussions in the first place.
In my opinion, there are several crucial differences between those situations:
1. The final game is not the middle one. And as of now, the probability of allying with Cerberus in ME3 end tends to minus infinity.
2. Not working together is not the same as killing each other.
3. There is no reason whatsoever to be attached to the Council or the Alliance, since they've done nothing to aid Shepard in the war with the Reapers, in fact they hindered Shepard to the best of their ability, and they weren't the ones who brought Shepard back from the dead. They've never been allies in the first place.
4. TIM is a person, not an organization, so the personal bond my Shepard shares with him is essentially different from any bond Shepard could in theory have with any faction. I have a personal attachment to TIM that's much stronger than any of the attachments to any of other characters, not to mention LIs.
5. Cerberus has a clear agenda about saving human lives. That's exactly what my Shepard's fighting for. Even in theory, I cannot see Shepard fighting for the aliens rather than for humanity. Shepard is canonically fighting for the Earth. That's Shepard's prime motivation. Hence, not only we share with Cerberus the history of actual alliance and a possible emotional connection, none of which is possible with the Council or the Alliance - we also share the ideas.
Yes, I believe it makes Cerberus situation very, very different. At least for people who wanted to work together with them.