From ME 1, Saren Himself states that the more control that Sovereign exerts, the less capable the subject becomes.
The time period from betwen Thessia and Activating the Crucible is anywhere from just under 24 hours to almost 5 days (depending on the locations of the various fleets, wether Shepard did anything in the meantime, etc), and since it is wartime, the sooner the better.
Also, Shepard was proven DEAD for almost 2 years. Reapers can control dead organic material that has been previously implanted, yes, but indoctrination itself has never been proven to be able to affect the dead (or why can we kill husks, mauraders, etc?), nor has it been proven that indoctrination can effect non-organic (say, a metal I-Beam) materials. Even the GETH had to be re-programmed.
Finally, Shepard can NEVER be fully indoctrinated. This is NOT immunity for Shepard, only high resistance. THere is a reason for this: The PLAYER. That's right. The person sitting at a keyboard, or sitting at a console, isn't indoctrinated, are they?
Are YOU who reads this indoctrinated?