I wish to use the pigpio C library which requires that the daemon is not running. My application will be in an embedded standalone system and I cannot therefore kill the daemon.
It depends on how it was started in the first place:
If it was started as a service on Raspbian use the following command:
sudo systemctl disable pigpiod
Assuming you followed this description to add pigpiod to the crontab:
sudo crontab -eagain to remove this line and have it not started on reboot.