What's happening here is that the writer is dramatising, through character exposition, the ethical issues in the situation. Doctor Who takes up a rather flip technological proposal which Clara had first suggested. "If you can't save them all, save who you can. The Tardis. It's a lifeboat, isn't it? Not everybody has to die." She said that. She now plays devil's advocate. She feels this is a half-baked idea. There is an author's subtext that Doctor Who needs to try harder to find a better solution. And he eventually does. Just let the trees take care of it. I'll assume that we're still conveniently ignoring the ridiculous technobabble that passes for scientific reasoning in Doctor Who. We never complain about that because it's just entertainment.
Like the Bible, the author can be wrong. You can treat every episode as sacrosanct with onus on the viewer to rightfully agree with every action taken and every line uttered, or you can view an episode as what it is intended to be.
All of it is entertainment, entertainment isn't by definition shallow. What you get from it comes from how engaging you find it. And the technobabble can also go horribly wrong where it stretches credibility too far, as in Kill The Moon, or involves just waving a Sonic Screwdriver when you have written yourself into a corner. Getting complained about just the same.
In The Forest Of The Night was a story shoehorned into a show which didn't suit it, during a series that didn't fit it, requiring the characters to also be shoehorned into it. Causing a host of problems when viewed as what it is, entertainment and just one part of a larger whole.
It's nice you liked it, but there are plenty of people who didn't. Somewhere out there is someone trying to explain the deeper intent of the writers of Under The Dome, and how it was all a misunderstood masterpiece that we could all take life-lessons from, and I'd be quite concerned for them.
