I guess this is where the faith in Bioware comes in.
One possible outcome:
Red beam/High Effective Military Strength: The Reapers used up a lot of energy trying (and failing) to take over Shepard, and lose the battle of Earth. Shepard is then picked up, becomes even more of a Messiah; the massive moral boost, increased understanding and Reaper disarray leads the Reapers to be stormed out of the galaxy.
Red/Low EMS: Reapers use a lot of energy, but still win the Battle of Earth. Shepard is picked up by stealthy reconnaissance teams and leads a guerilla war against the weakened Reapers. Reapers have the upper hand but all is not lost yet.
Green/High EMS: Reapers use energy (but less), lost battle of Earth. Shepard is resurrected by the victorious forces. During Shepard's victory address to all forces, the Reapers show their hand and reveal him to be indoctrinated, and he proclaims organics doomed. He then kills himself, Saren style (some fight was left in him). The demoralised organics continue the fight versus somewhat weakened Reapers. Upper hand to reapers, but all not lost for a little while.
Green/Low EMS: Reapers win the battle of Earth, recover Shepard (now their asset) - he gives doom speech to all the organics, but kills himself as before. Reapers eventually win out, thanks to weak and demoralised organic forces.
Blue/High EMS: Reapers lose battle of Earth, but during the victory address Shepard goes totally rogue, escapes and then leads the Reapers to crush the organics.
Blue/Low EMS: Reapers recover Shepard, use him as a general, fighter and demoralising icon to utterly crush all organics.
Crucible turns out to be Reaper propaganda for the purposes of drawing enemies into a pitched battle, and in this case, converting Shepard - the true superweapon (...) which may ultimately prove too much for them to handle. This allows scope for scenes of your rainbow coalition to be seen fighting the Reapers (if appropriate) and what happens to your crew afterwards. Only in the Red Scenarios is there any possibility of the player retaining control of Shepard.
Whoops, got a bit carried away. Basically in answer to you question - that's where my faith comes in. I reckon the IT ending is more salvageable/plausible than what currently exists.