Doctor Who: 14 Cool Details Revealed In Steven Moffat's Wedding Of River Song Commentary

In an act of cold-blooded badassery, Madame Kovarian is killed by Amy Pond towards the end of the episode, with Amy affixing Kovarian's electrified eye drive to her face and leaving her for dead. Quite deserved, considering that she kidnapped Amy's child.

While discussing Kovarian's fate during the commentary, Barber mentions that a couple of different endings for the character were shot, and Moffat notes that her death was actually a "very late rewrite".

Well, to be clear, her death was always going to happen, but the circumstances of it weren't decided upon until long after the script had been finalised.

Moffat says that he and executive producer Piers Wenger both agreed that simply killing off Kovarian wasn't enough (Moffat doesn't go into further detail about this, but we assume that Kovarian originally died due to her electrified eye drive, like everybody else) so they decided to have Amy murder her instead. Different versions of this outcome were shot, and in the end, the "cruel" one was chosen.

Of course, it's worth pointing out that the manner of Kovarian's death doesn't matter in the slightest, considering that this timeline is wiped out at the end of the episode.