well, shep reaches the control panel or whatever of the catalyst, and has the power to unleash the macguffin on the macguffinators. harbinger (who according to the theory has been trying to indoctrinate shep all through the game BEHIND THE SCENES) is too far away to blast them (but close enough to indoctrinate) and tricks shepard into doing something, w/e.
I'm not sure anyone has been trying to argue that Harbinger has been trying to indoctrinate Shepard through the
entire game (although we should be aware of the fact that Shepard has spent a good deal of time around Reaper tech, which was enough to indoctrinate a few people).
There is no reason to think, for instance, that the dream sequences are a subtle form of indoctrination. Personally, I see them as visual indications that Shepard possesses an internal psychological state marked by fear and doubt - and the child serves as a symbol of everything that could be destroyed if she fails. That's the setup: Shepard
does dream,
does doubt,
does use the kid as an embodiment of everything she holds dear and which could be taken away with just one wrong choice. These are all elements that are primed to be manipulated by creatures well known for their manipulative practices. And considering that Shepard has been, and in London, is surrounded by Reapers, it seems sensible that they would strike at her fragility.
Could they have just blown up her body instead of trying to perform an elaborate lie in order to indoctrinate her? Sure. But considering Harbinger's apparent love of mind games and how the importance of Shepard's life is fighting for unity and self-determination, it's thematically meaningful that the Reapers try to claim her as a trophy. If they can mentally topple Shepard, the one person who seems to resist their grand plan, then it is a symbol of their ultimate power over organic life. After all, there are multiple instances in which Shepard is referred to as an icon that inspires hope in others, and multiple characters recognize that crushing hope is the best way to conquer an enemy.
Also, it's just as unreasonable to weave these elements together into an indoctrination theory as it is to propose that "it isn't in Bioware's style." Both are attempts at creating patterns out of disparate elements. But the indoctrination theory relies on nothing more than the "text" itself, while the "lol Bioware can't write" idea relies on a number of assumptions: that every Bioware project must conform to the same standards, ideas and themes; that every Bioware writer is the same, and will write the same in every project; and that you have a clear understanding of the game's development, the writer's mindset and the team's intent on rejecting or embracing fan expectations. I see the latter as quite a bit more risky than the former.
