How to set up linux watchdog daemon with Intel 6300esb
The answer to your question was in the watchdog man page.
The watchdog daemon can be stopped without causing a reboot if the device /dev/watchdog is closed correctly, unless your kernel is compiled with the CONFIG_WATCHDOG_NOWAYOUT option enabled.
Since CONFIG_WATCHDOG_NOWAYOUT is not set according to your log message:
i6300ESB timer: initialized (0xffffc900008b8000). heartbeat=30 sec (nowayout=0)
then shutting down the watchdog daemon doesn't have the result you want. So now you know what to do.