That scene at the end of “The Family of Blood”, when the Doctor distributes weird Old Testament punishment to the antagonists of the piece? We never properly see what happened. It’s just narrated in voiceover — from the villain of the piece, no less. And it’s accompanied by over-the-top visuals. So I’m not sure how much weight we’re really supposed to give that version of events.
If you ever look in a mirror, any mirror, that’s where the sister is? Really? The son is left to dangle forever in a village cornfield — that presumably someone owns and will tend to eventually, or at least stumble across? Trapped forever in the event horizon of a star — and that’s keeping her alive? Likewise, kept alive by impossibly heavy chains? That somehow he’s just collapsing under as the Doctor walks away? The punishments don’t make the slightest sense, except in allegorical, fairy tale terms. And yet up to that point, the story tries to be fairly realistic within its own terms.
Furthermore, the way we’re shown the events, it’s all heightened. The colors are washed out, it’s grainy. The performance is all done for the camera, as if it’s illustrating the narration, rather than simply showing us a sequence of events. It’s a huge stylistic difference from the story to that point.
Anyway, how is the son narrating, and who is he narrating to, and why, if he was frozen forever?
It’s not just that the deeds don’t fit the character who we know, or who we’re shown throughout the story; it’s that the mode of storytelling doesn’t fit what we’ve seen first-hand to that point. If the sequence were intended literally, there would be much more to explain.
Maybe the Doctor did something to punish them, and maybe it was something along the lines of what we’re told, but all we have is this legend of the events, that seems to serve more to illustrate an impression or a concept of the Doctor, and of his behavior toward the antagonists, than it serves to illustrate a matter of fact. And frankly, again, we’ve just got the villain’s word for it all.
Unless there’s a sequel, we’ll never really know what happened; just that the Doctor impressed the hell out of Son-of-Mine.