I would set up the job to run in batch by using the at utility.
Code:
at -f script-name.sh now
Pipe the output to a log file. This is what I do with my Folding At Home software. I can read the log file to see the progress of the application.
You may need to install the at utility. It is not installed by default on all distributions.
The at utility will run the job in a system queue so it will not be affected if Gnome or X hangs unless the cause of your window manager hangup is due to a kernel level problem.
On the other hand it might be better to diagnose and fix the cause of your Gnome/X performance problem.