Looking at things from TIM's perspective, he had two choices if he wanted to stop the Reapers. He could work with the Alliance on the Crucible project, but nobody knows what that is or how it works. It could backfire, or just plain not work at all. It's a galactic Hail Mary born out of desperation with absolutely no guarantee of success. Meanwhile, Henry Lawson's lab is achieving promising results in controlling Reaper tech, and given more time there is a chance that they can scale that up to take control of actual Reapers. It's a desperate hope too, but at least there's actual science going into the project and not wishes and prayers. Knowing what TIM knows, it makes sense that he would pursue the option of control.
So why is he trying to block Shepard and the Alliance? Because he's trying to buy time. Cerberus has a target on their back due to their role in taking down the Collector base, but by disrupting Shepard's plans Cerberus are making themselves useful to the Reapers, thereby putting off their inevitable annihilation. TIM is hoping that he can buy Cerberus enough time to develop a way to control the Reapers.
At least, that's how TIM sees his actions. The truth is that he's slowly being indoctrinated and that's affecting his judgement. In the end, he runs out of time not because the Reapers ran out of targets and focused on Cerberus, but because the indoctrination overcame him.