It's a cool reading, but...
The whole theory suggests that the Reapers are attempting to prevent Shep from activating the Crucible and destroying them, by fighting a battle in his mind while he's lying in the rubble on Earth...unconscious...helpless...in clear sight of Harbinger...who is armed with ship-to-ship-weapons...
I'm seeing a more parsimonious way to stop Shep right here.
The battle could be fought in his mind independently. The reapers having planted their corruption in Shep's mind, and it works slowy wherever he is. To Harbinger, he might have just been another insignificant dead or almost dead organic lying in the rubble, provided it even bothered scanning the field for survivors.
Basically, there's no middle ground here. They've either pulled a brilliant move yet to be revealed, or they have writers which go from being relatively good (it's not life changing, but it's a fun story until the beam run) to unbelieavably inept in the last 10 minutes exactly, and the transition is a complete knife cut. I'm sure we'll find out eventually, but I'd agree with the notion that if Bioware hadn't planned this, they'd be smart to pretend that they did. They'd sell a lot more ME franchise additional stuff that way.