The more I think about it, the more the "hallucination/indoctrination" theory makes sense out of the ending's disparate elements.
For one, Harbinger opts to "direct this personally" by preventing Shepard from reaching the beam. He is practically standing over Shepard, who is physically and mentally beaten from the blast. We know that Harbinger loves to play mind games with Shepard and would consider her wholesale destruction a personal victory (I'm going with her, because FemShep is more badass). His presence also suggests that the Reapers want to avoid any risk of defeat.
When Shepard supposedly "wakes up" from the blast, we hear this over a comm: "Did we get anyone to the beam? Negative, our entire force was decimated." No one notices Shepard and Anderson moving toward the beam? Also, if you have the highest readiness rating (a requirement for the "Shepard lives" scene), your squadmates aren't seen dead in front of you (more on this later). Also, there is a new "death ring" around the screen as Shepard walks to the beam, made of water and blood, and it creates the impression of an eyeball "watching" this scene unfolding.
In ME1, Matriarch Benezia mentions that indoctrination is a voice inside your head, telling you things, showing you things.
In the bloody hallway, Shepard thinks it "makes sense" when Anderson describes his hallway as looking like the Collector Base. But why does that make sense? Because it's closest to her experience. They talk about the bodies being brought to the Citadel to be "processed," but that doesn't make sense, either - there's never been an indication that bodies are brought en masse to the citadel for such a purpose. This could be Shepard projecting her fear and experiences on the situation.
This is a little bit of a stretch, maybe, but the episode with Anderson and TIM could be Shepard "role playing" (tee hee) how she thinks she would handle that scenario. She imagines that she can convince TIM, whereas he has always demonstrated willfulness elsewhere in the game. Convincing him to kill himself is Shepard applying her memory of Saren to this new enemy.
When Admiral Hackett says "Shepard, the Crucible isn't working" over the comm, it would seem that he knows she's there. But really, how could that be possible? The earlier comm message gave no indication that she or Anderson were alive. It's impossible to tell if this exchange is real, or just fabricated in Shepard's mind. Maybe it's Shepard worried that something will go wrong - and this is the perfect opportunity for Harbinger to strike.
It is all too convenient that Shepard falls on to the elevator that takes her directly to the Catalyst, who just happens to maintain the form of the child that Shepard has been thinking about the whole game. The Catalyst offers shifty explanations and careful manipulations of choice to create, as Benezia said, a voice that seems real. The Catalyst misdirects Shepard from thinking that the "Citadel is the Catalyst," tries to convince her that being Reaperized is a form of "ascension" (where have we heard that before?), and that it's for the "good" of organics because they can't get along with synthetics (which has been proven to be false). When Shepard says "We'd rather keep our own form," he defensively shoots back, "No, you can't." And then offers his bullshit logic.
Shepard seems to uncharacteristically accept these explanations without question - but isn't that the point of indoctrination? Also, isn't it interesting that if you don't have high EMS, your only option is the "Destroy" ending? It would make sense that Harbinger gives you this only choice as a form of mockery, knowing you have insufficient strength to beat the Reapers. But as your power grows, your choices change - and the Catalyst specifically tries to direct you to the other choices. In the "Destroy" ending with high EMS, he suggestively says "Even you are partly synthetic..." as if to create the impression that destroying the Reapers is destroying yourself, along with the Geth and EDI (beings you care about, presumably). Before that even, he says "I know you thought about destroying us." How does he know? Of course, Harbinger would know.
In the "best" sequence, he offers "Destroy" first (interestingly, it's the "red" choice, as if it were bad), but then quickly shifts to the other two as "better" choices. Remember how he says "Yes [the Reapers will be destroyed], but the peace won't last"? Clear deflection. But his talk about "Control" is even more suspicious: he doesn't say "You could control us." He asks, "Or do you think you can control us?" He uses her knowledge of TIM to abuse a sense of guilt about him "being right after all," but then mocks TIM by saying "he could never control us because we already controlled him." This sounds a little like Harbinger hungering for the one person who could not be easily controlled. And maybe I'm reading a little into it, but when Shepard asks "But the Reapers will obey me?", he pauses briefly before saying "Yes" - as if he knows it's a lie.
Finally, he offers you the "Saren" choice - synthesis. If this choice sounds like the most bullshit, it's probably because it is. Isn't what the Reapers do technically "synthesis" - combining organic matter with synthetic parts? Isn't that what they did to Saren? We already know how that turned out, but the Catalyst presents it as one of the better choices (he claims it will lead to peace). In ME1, it only lead to Saren's betrayal.
It seems apparent that the Catalyst wants Shepard to waver from her original mission, to choose "Control" and become a Reaper, or choose "Synthesis" and probably also become a Reaper. Only in the "Destroy" ending, with a high-enough EMS, does Shepard wake up.
Thus, it's quite possible that the whole scene with Joker is Shepard imagining the impact of her choice - achieving success but destroying the mass relays (just as the Catalyst claimed, even though he never said why, but remember that the Reapers apparently created the mass relays and can use this as a point of manipulation). It is her mind combining the elements of her awareness (the earlier comm message telling everyone to pull back, the words of the Catalyst, perhaps her own concern for her crew) into a cohesive sequence.
tl;dr I think the "hallucination/indoctrination" interpretation could really work out in Bioware's favor, because its execution would be really clever - but perhaps too clever, since it would be so subtle and indefinite. Granted, even if this theory were true, it is no excuse for the complete lack of epilogue - but perhaps Bioware's intent was to keep it open.