First, I should say a few words about authorship. In organized internet fandom, there is a tendency to talk about popular works as if they were not self-contained texts, but windows into an alternate universe to which the "author" or director has privileged access. Although, of course, everyone knows intellectually that this is not true, this way of thinking persists on in fan circles as if the past hundred years of literary theory had not happened. The very term "canon" suggests that suggests that the religious metaphor is in full force; NGE is not a sci-fi series, but a divinely received text whose meaning can only be determined by the author-God. As Foucault says in "What is an Author?" :
Still, we can find through the ages certain constants in the rules of author construction. It seems, for example, that the manner in which literary criticism once defined the author - or, rather, constructed the figure of the author beginning with existing texts and discourses - is directly derived from the manner in which Christian tradition authenticated (or rejected) the texts at its disposal. In order to ‘rediscover’ an author in a work, modern criticism uses methods similar to those that Christian exegesis employed when trying to prove the value of a text by its author's saintliness.
Naturally, the concept of "authorship" is problematic enough for literary texts, let alone a collaborative effort such as a TV series or film. Although we often use "Anno" as shorthand for "studio Gainax circa 1995," these two are obviously not identical. Furthermore, even if Anno were the sole creator of NGE, who is to say that is interpretation of his own work has always remained constant? To cite an analogous example, Ridley Scott seems to have changed his mind several times with respect to the question of whether or not Rick Deckard, the hero of Blade Runner, is an android. According to Harrison Ford, the director once assured him that the character was human, but in recent interviews, Ridley Scott has claimed the opposite and re-edited the film accordingly.
This brings me to my main point: whether or not Misato killed Kaji is not an issue that can be determined by directorial fiat. Furthermore, it is very likely that the plot point in question was retconned in the DC edits. In the on-air and the DC episode, Misato's recovering her gun is followed mere seconds later by Kaji's murder. The scene in question can be viewed here: http://www.youtube.com/watch?v=OAPpMiDII3U#t=05m30s
Ignoring authorial fiat and later re-edits (such as the scene in the DC episodes where Kaji tells Fuyutsuki that Seele will likely kill him), it is quite clear that there is a causal link between these two scenes.
Misato's reaction makes all the more sense if she is Kaji's murderer; finding his message on the answering machine is a final, bitter irony. One may also note that there is no scene in which Misato learns of Kaji's murder, and his death does not seem to be common knowledge at Nerv.
