If you pay attention to the cinematic as the
Normandy lifts off, it looks like Harbinger
looks right at it. He
lets it go.
Check it out just before the two minute mark.
So, if that's the case, the IFF theory is wrong.
The "best" explanation - IMO - is that the command AI - the "starchild" (
stupid name, btw) -
wanted Shepard to reach the beam. It
was seeking a new solution, after all.
It's actually hard to say, because it
is open to many interpretations simply because the writing of the endings was the weakest of the game. The ending alone belies the assertion that the game "wasn't rushed". I think it's impossible to point at one thing and say "this is why", because there isn't any one thing. There are a couple of ways to look at it, and because the writing is so shallow, all or none of them are right - which just reinforces how poor it is.
The easiest interpretation is that "the minds of the reapers are unfathomable", and it was a simple whim on Harbinger's part. What does it care? At this point, the Reapers are in no danger of being stopped. They're "winning".
In other words, there
isn't a "good" explanation. It's more a "believe what you want" kinda thingy.