No, you cannot kill threads, you can only ask the thread to exit. If
the thread is in an infinite loop and thus paying no attention, you're
stuck. This is generally a limitation of the underlying POSIX thread
libraries.
Now, it might be possible to somehow use the Tcl event loop to say,
"Heh Tcl interpreter, stop that crap you're doing, execute this nice
clean thread shutdown command right now!" But that's just a vague
guess, I've never looked into it.
On any modern machine, it should not take "a minute or two" for an
OpenACS AOLserver to come back up, and if it is, it should be fixable.
Hm, if you tell Linux to kill the process id for that thread, I'm not
really sure what would happen. I'm 989 certain it will be a Bad
Thing, most likely the whole process will just die. It'd be worth
trying sometime (on a testing server of course).