I don't think that is accurate. The scene with Nylah wasn't there just for the lulz, it was there for Clarke to verbalize the fact that humanity needs Skycrew skills to survive. She is still working to keep humanity, any humanity, alive.
Before she knew about Octavia winning the fear was Luna would win and let no one in, so moving the Sky people in made total sense, Octavia was a massive long shot, that is repeatedly driven home in the last ep and Clarke has a bit of a 'nightbloods are awesome' blind spot. To Clarke, Octavia is as good as dead.
Once she knows about the miracle win the problem becomes if we let them in and they kick us out who will run the bunker? She doesn't at this point know that Octavia has been keeping the Skycrew betrayal a secret, she thinks everyone locked out knows about it, that they are going to be angry and will throw Skycrew out. We the viewer knows Octavia is working it out, Clarke doesn't. She is expecting to be met with Grounder violence, experience has shown her that to be true.
So what is to be done? The bunker is an advanced piece of technology, relying on the same skills Skycrew used in space, if it is left completely in the hands of the Grounders then what is left of humanity is completely doomed. They can't run it, they can't fix it, asking the grounder to run the bunker would be like asking a toddler to fix a a nuclear reactor. Opening the doors in Clarkes mind basically insures that no-one survives. Not her people, not grounders, not anyone.