Can I use a shell command to back up all domains but tell it to skip certain ones?
No, you can use the shell backup command below to back up a coma separated list of domains but you can not just tell it to skip certain ones. You need to specify the ones you want backed up and that list can be as long as you need.
/home/interworx/bin/backup.pex --domains=domain1,domain2,domain4,etc --file-path="/home/backups"
For more info on creating a SiteWorx backups from the shell, please visit this backup documentation.