A reboot will remove the config from the running configuration. If you watch the log you'll see the startup config error out as it tries to put in the lines of the config specific to the missing module. Just do a copy run start at that point and your startup config will reflect the change as well.
If you do not want to have to reboot the switch, put the line card back in, issue the module clear-config command and remove the module again. This will remove the configuration without a reboot.