First, check if /dev/md1 is already mounted. Maybe the FAI boot process (using dracut inside the initrd) detect this raid and activates it.
You may add a hook which wipes add signature of a soft raid using a simple script. For e.g. under https://fai-project.org/download/misc/ there are partition.WIPEDISKS and wipe-all These can also remove the disk partition label. -- regards Thomas