Hate to say it but it's really too much to speculate on.
In the end I don't see Cerberus adding that much to make too much a difference if they "played nice" and were never indoctrinated.
think about it. TIM could have been indoctrinated since way back from those comics. Before Cerberus even existed. If so Cerberus may have NEVER even existed....
if it did who's to say how much backing they would have had since we don't know if it's backers were also somehow indoctrinated.
it goes too far back to do any relevant speculation without making far too many assumptions about when where and how TIM was first indoctrinated.
Again had he never been indoctrinated who's to say Cerberus, as an organization, would have ever come to exist? TIM could just have grown old and fat at home...etc..etc..etc.
Not trying to derail your topic. But really, there's too many points at which he may have become indoctrinated and depending on those points Cerberus's very nature and existence is in question.
You may want to narrow your area if you really wish a coherent discussion on this. Say "assume TIM wasn't indoctrinated from the comics (sorry I can't think of that story/comic name) and cerberus existed as we saw it up to ME2" (or something of that nature.
But with TIM's indoctrination possibly going as far back as the comics (before CERBERUS exists) just brings up waaaaaaaay too many what-ifs as to whether cerberus even still existed as we know it or in some other form...if at all.