I find myself becoming more and more convinced by the 'Indoctrinated' interpretation. I don't usually buy into this sort of thing, and it may well be that I'm a) giving Bioware more credit than they perhaps deserve and b) rationalising it all away because I don't particularly like it/can't satisfactorily explain. I still find it compelling though. The reasons (and they're good ones) were made very clear in that social.bioware thread so I won't go through them again, but the single most important bit for me is that the 'Destroy' ending seems to be (correct me if I'm wrong (or don't because it casts the interpretation into doubt...)) the only one where we get any hint that Shepard is alive, with sufficient military strength. Also, it's on Earth, which lends further credence to the theory because otherwise (barring some sort of controlled-explosion scenario), the relays cannot have been destroyed.
If all this is true and they do indeed explain it all through DLC or somesuch, then that's despicable and dirty and horrible etc etc etc. But damn, as well as being something of a relief it would be a hell of a coup on their part. They might not even have originally intended it, but it would make sense for them to say they did even if that's the case. Whatever, I like the theory.