Okay, I just tried having a sleep delay in and the RasPi-zero appears to be booting with the correct time. The edited code is as follows.
modprobe rtc-ds1307
echo ds1307 0x68 | sudo tee /sys/class/i2c-adapter/i2c-1/new_device
sleep 1s
hwclock -s
I'm not fully happy with it... resetting the RTC is a somewhat of a pain.