Hmm. Well, you can archive Gallery somewhere and then restore it later.
Archiving it:
1. Download cleanup script from User Guide
2. Run cleanup script on albums directory
3. cd to the directory that contains "gallery" and "albums" and run:
"tar -czf gallery.tar.gz gallery albums"
4. "rm -rf gallery albums"
Now you have it all archived in "gallery.tar.gz". Put that somewhere, rebuild your site, etc.
Restore:
1. cd website
2. tar xzf gallery.tar.gz
3. re-run config wizard
4. rm gallery.tar.gz