The annoying Xorg beep can be disabled permanently. You only need to remove pcspkr from the kernel and add it in the blacklist:
Remove pcspkr from kernel:
$ sudo modprobe -r pcspkr
Blacklist the pcspkr:
Adding the pcspkr to blacklist will not load it anymore in the kernel.
Just append (as root) “blacklist pcspkr” in modprobe’s blacklist configuration file, like this:
$ sudo echo "blacklist pcspkr" >> /etc/modprobe.d/blacklist.conf
Add the Xorg beep back to your system:
Insert it back in the kernel modules:
$ sudo modprobe pcspkr
Remove (or comment) in /etc/modprobe.d/blacklist.conf, this line: blacklist pcspkr
Related reading: How to disable the Hardware Beep in FreeBSD.