I don't understand what the indoctrination theory has to do with you assertion that the game should cleave toward a fluid morality. Officially supporting the indoctrination idea doesn't have anything to do with morality. If you invest in the theory, your three choices would be read as:
- You break from indoctrination -- choosing to destroy the reapers represents your assertion of your own will
- You succumb to indoctrination -- choosing to control the reapers represents their tricking you into thinking that you can control them
- You succumb to indoctrination -- choosing to synthesize organic and synthetic life represents their tricking you into thinking that harmony can be obtained
Look at the dialogue with Saren from ME 1; he was tricked into thinking that some peace could be made with the reapears, that by going along with their plan, he would be spared, and could win some sort of reprieve for the other people of the galaxy, that the reapers would be content enslaving everyone. Your options are similar. The fact that Shepard is shown to be taking a breath only after the first choice would (according to the theory) support the idea that you have broken from indoctrination.
None of that has any bearing on morality. You can only argue that the moral choice is being ignored, or overridden, if you discount indocrtination theory, which presupposes that you feel the end of the game makes sense. It doesn't, though. Not at all. There may be a third option, one that is neither indoctrination, nor acceptance, but some other interpretation of the ending that also makes sense of all the nonsense we're given, but I haven't seen anything along those lines, and doubt there will be. You can choose to read the way the choices are displayed as being weighted toward one side of the morality spectrum, but they aren't as presented, and hardly are in consequence.
Ideally, we would receive DLC that picks up after the "ending" as we come out of the indoctrination sequence, and, depending upon our choice, are either under the reapers' control or are still standing against them. Further, we would be given a
real choice, with
real variation in consequences, based upon our own morals (or those we have instilled in our version of Shepard)--something like choosing between a usage of the Crucible that will destroy all the reapers, but may/probably also destroy Earth, or the combined fleet of the galaxy, or one that
may wipe out all repears, but will probably spare Earth/the galactic armies. etc...