Hm, ok. I double checked my recording of the final dialogue with TIM and my Shepard used mixed responses (neutral, renegade, then neutral/paragon). I guess I can't confirm it either way without going back to ME2 and replaying that part.
It's based upon that final exchange concerning the base itself. You can really question him as to his intentions. You can ask, "How will you use it?"
The crucial exchange comes right after that. If you pick the top response, "This doesn't feel right", or something like that, you get the "Abomination DERP" moment in ME3. If you choose the lower response, which I cannot presently remember, TIM continues his sales pitch. You can then, ultimately, destroy the base. If you avoid any choices that talk about it "feeling wrong", you should get the better response in ME3.
I know that, from my first playthrough, I feared that anyone trying to study the base would indoctrinated. It annoyed me that we couldn't vocalize that explicitly. I guess that fear turned out true, regardless of our choice. TIM's obvious Reaper eyes were also alarming. I liked working with him, since his character was so well done in ME2, but those eyes were always in the back of my mind. I wasn't aware, initially, of the comic book backstory as to how he'd acquired them. Again, that worst case scenario sure came true.