I haven't watched the entire episode closely enough to make this anything but an off the wall suggestion, but would it be possible to re-edit the episode to excise the Section 31 plot without eviscerating the story flow? Just a thought...
Possibly, but that wouldn't solve the problem, IMO. It'd really need a rewrite and additional material. And if we were going to do that, we'd be as well just remaking it. Which is actually an idea I've occasionally toyed with, but to be honest the story's been told, warts and all. It is what it is, and I'd rather move on to new material.