You can handle this in your shutdown script.
Just use, for instance, a flag file which, when present,
keeps the shutdown script from actually shutting down.
I started doing workarounds like this, but I don't like the idea of lock
files very much. Once upon a time (tm) my homebrew divx conversion
scripts were crashing every now and then, due to calculation errors.
Nowadays, I noticed some problems with vdrsync.pl, which doesn't seem to
like some DD-Recordings. Anyway, if you have to kill processes, lock
file handling is not always easy.