Saren does not try to prevent anything, he's trying to make the invasion less painful, or at least that's what he thinks. It's understandable.
Well, it has less to do with being painful or not but more to do with getting swept away from the face of time and space or getting the opportunity to have the genepool live on forever. As a GOD. (as long as that is the true story behind the Reaper's motives)
A funny sidenote: collector general and Shepard are alike in that they're manipulated into fulfilling their master's wishes (Harbinger, TIM) (also if you count Shepard's general stiffness and mortar brick attitude as a feature of the game). The only time where Shepard gets the choice to take a stand against TIM is the endgame decision of keeping or blowing up the base. I wonder if the Collector's general incompetence is to some extent due to the General's sneaky interventions or sheer will...
If you end up destroying the base it points to Shep and Gen taking an active stand against their overseer... that's how I see it. Die free or live as a slave, huh?
Otherwise a Saren/Sovereign situationarises (continues
) with Cerberus(TIM) and Shepard, ok you might have a technological edge over the Reapers but all the sweet talks about morality/dying free go to the hounds. It's even worse for renegades getting used like gullible henchmen.