My personal opinion was that it was cold blooded murder.
Brian took it more personally than I did; Neil was really the only friend he had on the Starbucket and represented fully 50% of people that he liked (since Nick died -- before that, it was only 33.3...%).
And so it came to pass that Neil suffered a catastrophic failure. He suddenly realized that something horrible was happening, that they were being invaded, or attacked, or the reactor was going, or something (he really wasn't sure what, and didn't feel that he had time to find out). So he transported/teleported/"beamed" the entire population of the Starbucket to "safety" and then shut himself and the entire TARDIS down.
I don't have a copy of the fragment where this all happens, or the preceeding fragments hinting at small failures in Neil's performance. I do have Brian's reaction to it.