I honestly cannot really be upset with that decision too much (to close the bunker).
While we as viewers rooted for Octavia of course (and I am sure Clarke was, too), Octavia emerging victorious was highly unlikely. So a beaten down, frustrated, scared, exhausted Clarke thought this was the pragmatic move. Add to this mix a wiley Jaha whispering in her ear and that’s how this ended up the way it did.
Don’t get me wrong, I wanted her to believe in Octavia and I definitely facepalmed about closing the door, but I can totally understand her motivation.
All that said, let’s see how I feel after my re-watch