Você deseja usar tmux kill-session
:
<~> $ tmux ls
0: 1 windows (created Sat Aug 17 00:03:56 2013) [80x23]
2: 1 windows (created Sat Aug 24 16:47:58 2013) [120x34]
<~> $ tmux kill-session -t 2
<~> $ tmux ls
0: 1 windows (created Sat Aug 17 00:03:56 2013) [80x23]