Intenta usar el ssh secuencia de escape de terminación de conexión.
En el ssh sesión, ingrese ~. (punto de tilde). No verá los caracteres cuando los escriba, pero la sesión terminará inmediatamente.
$ ~.
$ Connection to me.myhost.com closed.
Desde man 1 ssh
The supported escapes (assuming the default ‘~’) are:
~. Disconnect.
~^Z Background ssh.
~# List forwarded connections.
~& Background ssh at logout when waiting for forwarded
connection / X11 sessions to terminate.
~? Display a list of escape characters.
~B Send a BREAK to the remote system (only useful for SSH protocol
version 2 and if the peer supports it).
~C Open command line. Currently this allows the addition of port
forwardings using the -L, -R and -D options (see above). It also
allows the cancellation of existing remote port-forwardings using
-KR[bind_address:]port. !command allows the user to execute a
local command if the PermitLocalCommand option is enabled in
ssh_config(5). Basic help is available, using the -h option.
~R Request rekeying of the connection (only useful for SSH protocol
version 2 and if the peer supports it).
Simplemente presione Ctrl D y lo desconectará allí para mantener presionada la tecla ctrl y presionar "d" hasta que desaparezca la ventana.
Simplemente cierre PuTTY. (Alt +F4 por defecto IIRC.)