I didn't like the ending either
I know this isn't Star Trek but if I learned anything from that series it's "The needs of the many outweigh the needs of the few or the one."
I hate that people must be sacrificed to protect others but if it must be done so be it. Apparently, these surviving junkies had to play the selfish card and cause more death and chaos because Whendon thought that would be a better ending.
Go Figure!!