Something about Harry's deductions in Ch.46 smells fishy to me. It could be that he didn't consider that two or more professors could have been present at the revealing of the prophecy. It could be that he automatically assumed the prophecy must have been freshly produced, rather than having been found in an old book as is usually proper. It could be that "It was Snape who told Voldemort about the prophecy (not knowing whom it spoke of)" does not in any way follow from "At some point, Snape begged Voldemort to spare Lily's life".

It could be a number of such things, but they could be explained away somehow: the real problem, I think, is that this looks like one of those magical trains of thought that bad crime fiction writers give their Holmes-ripoff protagonists, wherein the author starts from the solution and then, looking backwards, draws a path that enables the character to figure it out.

But it ends up looking fake, as it does now, because the character runs straight from the minimal facts he has to the hindsight-correct solution. This is not how an intelligent, realistic character thinks: before moving on to the next deduction, you try to take into consideration as many possibilities as you can, before you risk wasting your time or - gasp - take action using your very first idea as a logical premise.

And yet here, before the "Perhaps Dumbledore..." passage, Harry spends almost an entire page nose in the air, following his author-granted Magical Truth Compass. He doesn't even mention any alternatives, even though there are a boatload of those. Of course he knows Voldemort's and the Death Eaters' psychology well enough that he can confidently interpret his disinterest in Lily as a servant's prayer. What else could it possibly have been?

I don't think Harry's deduction chain needs to be scrapped, but I definitely think it needs more work, because in its current state it shattered my suspension of disbelief, hard. Make him consider and dismiss more options along the way, or make him express some thought along the lines of "It was a shaky conclusion, and he could have been mistaken or misinformed on any number of points... but if it was correct, the implications were dramatic, and if it wasn't, asking those questions would cause no harm, and might still provide important clues", or even better, both.

PS: The above applies even if the MoR-truth is actually different and Harry is therefore tragically mistaken. The narrative would be a lot more interesting, but the undeserved confidence of that train of thought would remain an artistic problem.