MacIntyre himself would answer (and does, in the pages of After Virtue), that this critique can only be made on the basis of Enlightenment presuppositions about our capacity for seeing the truth objectively, without reference to our own moral positions. And this sort of Enlightenment stance is precisely what MacIntyre is writing to rebutt: we cannot think about the past, or about anything (he says), without making moral judgments. There is no such thing as a perfectly objective standpoint from which to view what has gone before us.
So who's right? I take it (for now) that the truth lies between the two positions: that it must be possible to make some kinds of "objective" judgments sometimes--judgments which are true without respect to our moral stances--but, on the other hand, that we really do this much less than we think. Surely we can, that is, make objective assertions about whether this or that happened in the past, and to whom and with respect to what, just as we might make similar assertions about the chemical structure of certain elements, etc. (MacIntyre, in other places, seems to deny even this sort of claim.) But as soon as we begin to think any larger sorts of thoughts, to make any larger kinds of theories--certainly about history or causality in human affairs, we are necessarily going to have to rely upon our moral understanding: our view of human nature, its ends, its principles, etc. Because we must, it seems, judge human events in terms of what humans are, and "what humans are" cannot be defined without reference to what humans ought to be--without reference to our status as moral beings.
That, at least, is where I find myself just now. Closer to MacIntyre than to the student, I suppose, though I'm still trying to negotiate the space.